Psyllid ID: psy938

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-
Protein Sequence
MEVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGDR
Secondary Structure (PSIPRED)
ccccccEEEcccccccccccccccccccEEEEccccccccHHHHHccccccHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccHHHHHHHcccccEEEEcccccccHHHHHHHccccccHHHHHHHHHHccEEEccEEccccccccccccccccccEEEEEcccccEEEEEEccccHHHHHHHHHHccccEEEEEcccc
Secondary Structure Prediction (SSPRO)
ccccEEEEEEEcccEcccccEccEccccEcEcccccccHHHHHHHHHcccHHHHHHHHHHHccccHHHHHHHHHHHHHcHHHcHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccHHHccHHHHHHHHHccccccEccccccccccHHHHHHHccccccHHHHHHHHHccEEEEcccEEcccccEEcccHHHccccEEEEEcccHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEccc
Coil and Loop (DISEMBL)
mevtgdgglttpiiesesgekfgKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFkrqnehkpeERRAQKKLAEDLTLlvhgeeglksAKLATQALYSQdldslgslnatdasrifpgARIVELLMEPGMSMLELSLatkcfprdkeanltiseggfyvnykkvqnpqevlspsahilpnsLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGDR
Flexible Loop (DISEMBL)
mevtgdgglttpiiesesgekfGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFkrqnehkpeerRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKsaniiakshrydmyiVTIGDR
Low Complexity Region (SEG)
MEVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVsaniiaksaniiaksaniiaksHRYDMYIVTIGDR
Disordered region (IsUnstruct)
***************************NAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIED*********************LTLLVHGEEGL**AKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTI***
Disordered Region (DISOPRED)
**VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFK*********RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGD*
Disordered Region (DISEMBL)
********LTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKR************KKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGDR
Disordered Region (DISPRO)
*EVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGDR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRYDMYIVTIGDR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	241	2.2.26 [Sep-21-2011]
Q9W107	464	Probable tyrosine--tRNA l	yes	N/A	0.817	0.424	0.527	1e-55
Q5I0L3	471	Tyrosine--tRNA ligase, mi	yes	N/A	0.817	0.418	0.416	1e-39
Q8BYL4	472	Tyrosine--tRNA ligase, mi	yes	N/A	0.817	0.417	0.411	1e-39
Q9Y2Z4	477	Tyrosine--tRNA ligase, mi	yes	N/A	0.817	0.412	0.411	2e-38
Q65G35	421	Tyrosine--tRNA ligase 1 O	yes	N/A	0.796	0.456	0.357	6e-28
Q74LL0	420	Tyrosine--tRNA ligase OS=	yes	N/A	0.751	0.430	0.367	7e-28
Q5FMI6	420	Tyrosine--tRNA ligase OS=	yes	N/A	0.721	0.414	0.385	2e-27
Q8CXA5	428	Tyrosine--tRNA ligase OS=	yes	N/A	0.792	0.446	0.352	6e-27
A6T9Y5	428	Tyrosine--tRNA ligase OS=	yes	N/A	0.792	0.446	0.352	2e-26
P00952	419	Tyrosine--tRNA ligase OS=	N/A	N/A	0.784	0.451	0.358	2e-26

>sp|Q9W107|SYYM_DROME Probable tyrosine--tRNA ligase, mitochondrial OS=Drosophila melanogaster GN=CG16912 PE=2 SV=1

 Score =  216 bits (551), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 138/197 (70%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN +
Sbjct: 317 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAELNLS 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 437 LTTGVHILRNGISLLRV 453

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).
Drosophila melanogaster (taxid: 7227)
EC: 6EC: .EC: 1EC: .EC: 1EC: .EC: 1

>sp|Q5I0L3|SYYM_RAT Tyrosine--tRNA ligase, mitochondrial OS=Rattus norvegicus GN=Yars2 PE=2 SV=1

 Score =  163 bits (412), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 82/197 (41%), Positives = 123/197 (62%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T P+I S +G K GKSA NA+WL+ + +S FELYQ+ IR +D  V   LKLF+F  L 
Sbjct: 262 GITVPLITSTTGAKLGKSAGNAVWLNREKTSPFELYQFFIRQQDDSVERYLKLFTFLPLP 321

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I+   + +  +PE+R AQK+LA ++T LVHG+EGL SAK  TQALY   +++L  ++  
Sbjct: 322 EIDHIMQLHVKEPEKRIAQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIEALEVMSDQ 381

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +   +F  A   EL+++PG S+++        P        I+EGG  +N+++V NP+ V
Sbjct: 382 ELKELFKEASFSELVLDPGTSVIDTCRKANAIPDGPRGYRMITEGGVSINHRQVTNPESV 441

Query: 188 LSPSAHILPNSLTLLRV 204
           L    HIL N L+LL++
Sbjct: 442 LVIGQHILKNGLSLLKI 458

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q8BYL4|SYYM_MOUSE Tyrosine--tRNA ligase, mitochondrial OS=Mus musculus GN=Yars2 PE=2 SV=2

 Score =  162 bits (411), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 123/197 (62%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T P+I S +G K GKSA NA+WL+ + +S FELYQ+ +R +D  V   LKLF+F  L 
Sbjct: 263 GITVPLITSTTGAKLGKSAGNAVWLNREKTSPFELYQFFVRQQDDSVERYLKLFTFLPLP 322

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I+   + +  +PE+R AQK+LA ++T LVHG+EGL SAK  TQALY   +++L  ++  
Sbjct: 323 EIDHIMQLHVKEPEKRVAQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIEALEVMSDQ 382

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +   +F  A   EL+++PG S+++        P        I+EGG  +N+++V NP+ V
Sbjct: 383 ELKELFKEASFSELVLDPGTSVIDTCRKANAIPDGPRGYRMITEGGVSINHRQVTNPESV 442

Query: 188 LSPSAHILPNSLTLLRV 204
           L    HIL N L+LL++
Sbjct: 443 LVIGQHILKNGLSLLKI 459

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q9Y2Z4|SYYM_HUMAN Tyrosine--tRNA ligase, mitochondrial OS=Homo sapiens GN=YARS2 PE=1 SV=2

 Score =  159 bits (401), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 81/197 (41%), Positives = 116/197 (58%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T P+I S +G K GKSA NA+WL+   +S FELYQ+ +R  D  V   LKLF+F  L 
Sbjct: 268 GITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLP 327

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I+   + +  +PE R  QK+LA ++T LVHG EGL SAK  TQALY   +D+L  ++  
Sbjct: 328 EIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQALYHSSIDALEVMSDQ 387

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +   +F  A   E  ++PG S+L+        P        I+EGG  +N+++V NP+ V
Sbjct: 388 ELKELFKEAPFSEFFLDPGTSVLDTCRKANAIPDGPRGYRMITEGGVSINHQQVTNPESV 447

Query: 188 LSPSAHILPNSLTLLRV 204
           L    HIL N L+LL++
Sbjct: 448 LIVGQHILKNGLSLLKI 464

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q65G35|SYY1_BACLD Tyrosine--tRNA ligase 1 OS=Bacillus licheniformis (strain DSM 13 / ATCC 14580) GN=tyrS1 PE=3 SV=2

 Score =  124 bits (311), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 70/196 (35%), Positives = 110/196 (56%), Gaps = 4/196 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+   AIWLD + +S++E YQ+ I T D +V   LK F+F S  
Sbjct: 218 GLTIPLVTKADGTKFGKTEGGAIWLDKEKTSAYEFYQFWINTDDRDVVKYLKYFTFLSKE 277

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IED   + E  PE+R AQK+LAE++T+LVHG E  + A   ++AL+S D+     L A 
Sbjct: 278 EIEDLAEKTETAPEKREAQKRLAEEVTVLVHGREAFEQAVNISKALFSGDIK---QLTAE 334

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +    F G   +E+     + ++E+ + +K  P  ++A   I+ G  YVN ++  +  +V
Sbjct: 335 EVKVGFKGVPSLEVEKADELPLVEILVQSKLSPSKRQAREDITNGAVYVNGERRTDVADV 394

Query: 188 LSPSAHILPNSLTLLR 203
           L+    I     T++R
Sbjct: 395 LTADDRI-EGQFTVIR 409

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Bacillus licheniformis (strain DSM 13 / ATCC 14580) (taxid: 279010)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q74LL0|SYY_LACJO Tyrosine--tRNA ligase OS=Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533) GN=tyrS PE=3 SV=2

 Score =  124 bits (310), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 68/185 (36%), Positives = 103/185 (55%), Gaps = 4/185 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGKSA  A+WLD + +S +E YQ+ I   D +V   LK F+F S  
Sbjct: 218 GLTIPLMLKADGTKFGKSAGGAVWLDPEKTSPYEFYQFWINQDDRDVVKYLKYFTFLSRE 277

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IED   + E +P +R AQK+LAE++T  VHGEEGLK A++ T+AL+S ++ SL      
Sbjct: 278 EIEDLAEKTEKEPWKRAAQKRLAEEVTKFVHGEEGLKEAQIITEALFSGNVKSLSVPQIE 337

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
            A +  P A           +++E  + TK  P  ++A   +  G  YVN ++  +   +
Sbjct: 338 QALKNAPSAEAT----HEAKNIVEFLVETKIEPSKRQAREDVKNGAIYVNGERQDDIDFI 393

Query: 188 LSPSA 192
           + P +
Sbjct: 394 IEPDS 398

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Lactobacillus johnsonii (strain CNCM I-12250 / La1 / NCC 533) (taxid: 257314)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q5FMI6|SYY_LACAC Tyrosine--tRNA ligase OS=Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) GN=tyrS PE=3 SV=1

 Score =  122 bits (306), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 74/192 (38%), Positives = 103/192 (53%), Gaps = 18/192 (9%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGKSA  A+WLD + +S +E YQ+ I   D +V   LK F+F S  
Sbjct: 218 GLTIPLMLKADGTKFGKSAGGAVWLDPEKTSPYEFYQFWINQDDRDVVKYLKYFTFLSHE 277

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSL------ 121
            IED   + E +P +R AQKKLAE++T  VHGEEGLK A++ T AL+S D+ +L      
Sbjct: 278 EIEDLAEKTEKEPWKRAAQKKLAEEVTKFVHGEEGLKEAQMITDALFSGDIKNLSVTQIE 337

Query: 122 -GSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKK 180
            G  NA  A        IV+ L++           TK  P  ++A   +  G  YVN  +
Sbjct: 338 QGLKNAPSAEAGSEKKNIVDFLVD-----------TKIEPSKRQAREDVKNGAIYVNGDR 386

Query: 181 VQNPQEVLSPSA 192
            Q+    + PS+
Sbjct: 387 EQSVDFEVDPSS 398

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM) (taxid: 272621)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|Q8CXA5|SYY_OCEIH Tyrosine--tRNA ligase OS=Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831) GN=tyrS PE=3 SV=1

 Score =  120 bits (302), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 69/196 (35%), Positives = 108/196 (55%), Gaps = 5/196 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+A NAIWLD+  +S +E YQ+   T D +V   ++ F+F S+ 
Sbjct: 223 GLTVPLITKADGTKFGKTAGNAIWLDASKTSPYEFYQFWFNTDDRDVIRFIRYFTFLSVE 282

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I + +++ E +PE+R AQK+LAE++T  VH E  L+ AK  T AL+S D+  L      
Sbjct: 283 EITELEKEVETQPEKRVAQKRLAEEMTKTVHDEAALEQAKRITNALFSGDIKQLNVEEVE 342

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
            A +  P   I     EP + +++L +  K     ++A   +  G  Y+N ++VQ+    
Sbjct: 343 QAFKDVPNHIITR---EP-VGLIDLLVDAKISSSKRQAREDVKNGAIYINGERVQDMNYH 398

Query: 188 LSPSAHILPNSLTLLR 203
           +    H L N  T++R
Sbjct: 399 VEEKDH-LGNKFTVVR 413

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831) (taxid: 221109)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|A6T9Y5|SYY_KLEP7 Tyrosine--tRNA ligase OS=Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) GN=tyrS PE=3 SV=1

 Score =  119 bits (298), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 69/196 (35%), Positives = 112/196 (57%), Gaps = 5/196 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F  +A
Sbjct: 226 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMDIA 285

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK  T++L++ +L  L   +  
Sbjct: 286 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLEAAKRITESLFNGNLSDLSEADFE 345

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
             ++   G  ++E  ME G  +L+  + ++  P   +A  T++     +N +K  +P+ V
Sbjct: 346 QLAQ--DGVPMIE--MEKGADLLQALVDSELQPSRGQARKTVASNAVTINGEKQADPEYV 401

Query: 188 LSPSAHILPNSLTLLR 203
            S S  +     TLLR
Sbjct: 402 FSDSDRLF-GRYTLLR 416

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (taxid: 272620)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

>sp|P00952|SYY_GEOSE Tyrosine--tRNA ligase OS=Geobacillus stearothermophilus GN=tyrS PE=1 SV=1

 Score =  119 bits (298), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 71/198 (35%), Positives = 111/198 (56%), Gaps = 9/198 (4%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A   ++AL+S D+ +L      
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRISEALFSGDIANL------ 330

Query: 128 DASRIFPGARIVELLMEPG--MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQ 185
            A+ I  G + V   +  G  + ++EL ++    P  ++A   I  G  YVN +++Q+  
Sbjct: 331 TAAEIEQGFKDVPSFVHEGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVG 390

Query: 186 EVLSPSAHILPNSLTLLR 203
            +L+ + H L    T++R
Sbjct: 391 AILT-AEHRLEGRFTVIR 407

Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).

Geobacillus stearothermophilus (taxid: 1422)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	241
195027758	464	GH21538 [Drosophila grimshawi] gi|193902	0.817	0.424	0.522	1e-54
195120199	464	GI19509 [Drosophila mojavensis] gi|19390	0.817	0.424	0.527	2e-54
16768608	442	GM10508p [Drosophila melanogaster]	0.817	0.445	0.527	4e-54
20130383	464	CG16912 [Drosophila melanogaster] gi|504	0.817	0.424	0.527	5e-54
195353270	464	GM11790 [Drosophila sechellia] gi|194127	0.817	0.424	0.527	7e-54
194886727	464	GG19890 [Drosophila erecta] gi|190659858	0.817	0.424	0.527	1e-53
195489803	464	GE11414 [Drosophila yakuba] gi|194178993	0.817	0.424	0.527	2e-53
195380215	464	GJ21079 [Drosophila virilis] gi|19414366	0.817	0.424	0.512	3e-53
125809705	464	GA14214 [Drosophila pseudoobscura pseudo	0.817	0.424	0.522	3e-53
195155049	337	GL17697 [Drosophila persimilis] gi|19411	0.817	0.584	0.522	3e-53

>gi|195027758|ref|XP_001986749.1| GH21538 [Drosophila grimshawi] gi|193902749|gb|EDW01616.1| GH21538 [Drosophila grimshawi]

 Score =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 103/197 (52%), Positives = 140/197 (71%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T PI+ +E G+KFGKSA NA+WLD K +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GMTLPIVTNEEGDKFGKSAGNAVWLDEKKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  ++D L  LN T
Sbjct: 317 EVEQLMREHAKEPEKRKAQTLLAEDVTLLVHGEHGLKQAERVTNALYKGNVDGLAELNYT 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V++L EPGMS+L+L++  KCFP + +A   I+ GGFY+N K+VQN  EV
Sbjct: 377 EIKQTFQGATVVDILTEPGMSILQLAMKAKCFPTETDAVRIINAGGFYINQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           ++   HIL N ++LLRV
Sbjct: 437 ITTGIHILRNGVSLLRV 453

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195120199|ref|XP_002004616.1| GI19509 [Drosophila mojavensis] gi|193909684|gb|EDW08551.1| GI19509 [Drosophila mojavensis]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 139/197 (70%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT PI+ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  LA
Sbjct: 257 GLTLPIVTNEEGDKFGKSAGNAVWLDESKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLA 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            ++   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  ++D L  LN  
Sbjct: 317 EVDQLMREHAKEPEKRKAQTLLAEDVTLLVHGEHGLKQAERVTNALYKGNVDGLAELNYE 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V+LL EPGMS+L+L++  KCFP + +A   IS GGFY+N K+VQN  EV
Sbjct: 377 EIKQTFQGATVVDLLTEPGMSILQLAMKAKCFPTESDAVRIISAGGFYINQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           ++   HIL N ++LLRV
Sbjct: 437 ITTGIHILRNGVSLLRV 453

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|16768608|gb|AAL28523.1| GM10508p [Drosophila melanogaster]

 Score =  216 bits (551), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 138/197 (70%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 235 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 294

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN +
Sbjct: 295 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAELNLS 354

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 355 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 414

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 415 LTTGVHILRNGISLLRV 431

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|20130383|ref|NP_611967.1| CG16912 [Drosophila melanogaster] gi|50401704|sp|Q9W107.1|SYYM_DROME RecName: Full=Probable tyrosine--tRNA ligase, mitochondrial; AltName: Full=Tyrosyl-tRNA synthetase; Short=TyrRS; Flags: Precursor gi|7291852|gb|AAF47271.1| CG16912 [Drosophila melanogaster] gi|157816396|gb|ABV82192.1| FI02013p [Drosophila melanogaster]

 Score =  216 bits (551), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 138/197 (70%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN +
Sbjct: 317 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAELNLS 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 437 LTTGVHILRNGISLLRV 453

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195353270|ref|XP_002043128.1| GM11790 [Drosophila sechellia] gi|194127216|gb|EDW49259.1| GM11790 [Drosophila sechellia]

 Score =  216 bits (550), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 137/197 (69%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GLTLPLVTTEEGDKFGKSAGNAVWLDCNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN  
Sbjct: 317 QVEQLMREHTREPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAQLNLP 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 437 LTTGVHILRNGISLLRV 453

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194886727|ref|XP_001976671.1| GG19890 [Drosophila erecta] gi|190659858|gb|EDV57071.1| GG19890 [Drosophila erecta]

 Score =  215 bits (548), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 137/197 (69%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN  
Sbjct: 317 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAELNLP 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 437 LTTGVHILRNGISLLRV 453

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195489803|ref|XP_002092892.1| GE11414 [Drosophila yakuba] gi|194178993|gb|EDW92604.1| GE11414 [Drosophila yakuba]

 Score =  214 bits (545), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 104/197 (52%), Positives = 136/197 (69%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY   ++ L  LN  
Sbjct: 317 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGKVEGLAELNLP 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           L+   HIL N ++LLRV
Sbjct: 437 LTTGVHILRNGISLLRV 453

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195380215|ref|XP_002048866.1| GJ21079 [Drosophila virilis] gi|194143663|gb|EDW60059.1| GJ21079 [Drosophila virilis]

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 101/197 (51%), Positives = 138/197 (70%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T PI+ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct: 257 GMTLPIVTNEEGDKFGKSAGNAVWLDENKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  ++D L  LN  
Sbjct: 317 EVEQLMREHAKEPEKRKAQTLLAEDVTLLVHGEHGLKQAERVTNALYKGNVDGLAELNYA 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V++L EPGMS+L+L++  KCFP + +A   I+ GGFY+N K+VQN  EV
Sbjct: 377 EIKQTFQGAAVVDILTEPGMSILQLAMKAKCFPTETDAVRIINAGGFYINQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           ++   HIL N ++LLRV
Sbjct: 437 ITTGIHILRNGVSLLRV 453

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|125809705|ref|XP_001361216.1| GA14214 [Drosophila pseudoobscura pseudoobscura] gi|54636391|gb|EAL25794.1| GA14214 [Drosophila pseudoobscura pseudoobscura]

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 103/197 (52%), Positives = 137/197 (69%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T PI+ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSE   LLKLF+F  L 
Sbjct: 257 GMTLPIVTNEEGDKFGKSAGNAVWLDENKTSPFALYQFFLRMPDSEAEKLLKLFTFIPLT 316

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE   +++E +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY   +D L  LN  
Sbjct: 317 EIEQLMQEHEKEPEKRKAQTLLAEDVTLLVHGENGLKQAERVTNALYKGKVDGLAELNYA 376

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V+LL EPGMS+L+L++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 377 EIKQTFQGAAVVDLLTEPGMSILQLAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query: 188 LSPSAHILPNSLTLLRV 204
           ++   HIL N ++LLRV
Sbjct: 437 ITAGIHILRNGVSLLRV 453

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195155049|ref|XP_002018419.1| GL17697 [Drosophila persimilis] gi|194114215|gb|EDW36258.1| GL17697 [Drosophila persimilis]

 Score =  214 bits (544), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 103/197 (52%), Positives = 137/197 (69%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T PI+ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSE   LLKLF+F  L 
Sbjct: 130 GMTLPIVTNEEGDKFGKSAGNAVWLDENKTSPFALYQFFLRMPDSEAEKLLKLFTFIPLP 189

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE   +++E +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY   +D L  LN  
Sbjct: 190 EIEQLMQEHEKEPEKRKAQTLLAEDVTLLVHGENGLKQAERVTNALYKGKVDGLAELNYA 249

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F GA +V+LL EPGMS+L+L++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct: 250 EIKQTFQGAAVVDLLTEPGMSILQLAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 309

Query: 188 LSPSAHILPNSLTLLRV 204
           ++   HIL N ++LLRV
Sbjct: 310 ITAGIHILRNGVSLLRV 326

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	241
FB|FBgn0035064	464	CG16912 [Drosophila melanogast	0.817	0.424	0.527	3.1e-51
UNIPROTKB|E2RHU6	477	YARS2 "Uncharacterized protein	0.842	0.425	0.404	9.9e-39
RGD|1311696	471	Yars2 "tyrosyl-tRNA synthetase	0.842	0.430	0.409	4.3e-38
UNIPROTKB|I3L635	435	LOC100624597 "Uncharacterized	0.842	0.466	0.409	5.5e-38
MGI|MGI:1917370	472	Yars2 "tyrosyl-tRNA synthetase	0.842	0.430	0.404	5.5e-38
UNIPROTKB|A5D7G0	478	YARS2 "Uncharacterized protein	0.842	0.424	0.404	3e-37
UNIPROTKB|Q9Y2Z4	477	YARS2 "Tyrosine--tRNA ligase,	0.842	0.425	0.404	8e-37
ZFIN|ZDB-GENE-030131-6268	474	yars2 "tyrosyl-tRNA synthetase	0.817	0.415	0.390	1e-36
UNIPROTKB|E1C266	484	YARS2 "Uncharacterized protein	0.817	0.407	0.401	9.2e-36
UNIPROTKB|P0AGJ9	424	tyrS "tyrosyl-tRNA synthetase"	0.788	0.448	0.355	1.5e-26

FB|FBgn0035064 CG16912 [Drosophila melanogaster (taxid:7227)]

 Score = 532 (192.3 bits), Expect = 3.1e-51, P = 3.1e-51
 Identities = 104/197 (52%), Positives = 138/197 (70%)

Query:     8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
             GLT P++ +E G+KFGKSA NA+WLD   +S F LYQ+ +R  DSEV  LLKLF+F  L 
Sbjct:   257 GLTLPLVTTEEGDKFGKSAGNAVWLDGNKTSPFALYQFFLRMPDSEVEKLLKLFTFIPLP 316

Query:    68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
              +E   R++  +PE+R+AQ  LAED+TLLVHGE GLK A+  T ALY  +++ L  LN +
Sbjct:   317 QVEQLMREHTKEPEKRKAQTLLAEDVTLLVHGESGLKQAERVTNALYKGNVEGLAELNLS 376

Query:   128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
             +  + F GA +V LL EPGMS+LEL++  KCFP + +A   I+ GGFYVN K+VQN  EV
Sbjct:   377 EIQQTFQGATMVNLLTEPGMSILELAMKAKCFPTETDAVRIINAGGFYVNQKRVQNIAEV 436

Query:   188 LSPSAHILPNSLTLLRV 204
             L+   HIL N ++LLRV
Sbjct:   437 LTTGVHILRNGISLLRV 453

GO:0004831 "tyrosine-tRNA ligase activity" evidence=ISS

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006412 "translation" evidence=ISS

GO:0005739 "mitochondrion" evidence=ISS

UNIPROTKB|E2RHU6 YARS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 83/205 (40%), Positives = 130/205 (63%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             ++TG+   G+T P++ S +G K GKSA NA+WL+ + +S FELYQ+ +R +D+ V   LK
Sbjct:   260 KLTGEDVFGITVPLVTSTTGAKLGKSAGNAVWLNREKTSPFELYQFFVRQQDNLVERYLK 319

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + ++ +PE+R  QK+LA ++T LVHG+EGL SAK  TQALY   +D
Sbjct:   320 LFTFLPLPEIDHIMQLHDKEPEKRGPQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSID 379

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   EL+++PG S+L++       P        I+EGG  +N++
Sbjct:   380 ALEVMSDQELKELFKEASFSELVLDPGTSVLDICRKANAIPDGPRGYRMITEGGVSINHR 439

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   440 QVTNPESVLVVGQHILKNGLSLLKI 464

GO:0072545 "tyrosine binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

RGD|1311696 Yars2 "tyrosyl-tRNA synthetase 2 (mitochondrial)" [Rattus norvegicus (taxid:10116)]

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 84/205 (40%), Positives = 128/205 (62%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             ++TG+   G+T P+I S +G K GKSA NA+WL+ + +S FELYQ+ IR +D  V   LK
Sbjct:   254 KLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNREKTSPFELYQFFIRQQDDSVERYLK 313

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + +  +PE+R AQK+LA ++T LVHG+EGL SAK  TQALY   ++
Sbjct:   314 LFTFLPLPEIDHIMQLHVKEPEKRIAQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIE 373

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   EL+++PG S+++        P        I+EGG  +N++
Sbjct:   374 ALEVMSDQELKELFKEASFSELVLDPGTSVIDTCRKANAIPDGPRGYRMITEGGVSINHR 433

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   434 QVTNPESVLVIGQHILKNGLSLLKI 458

GO:0000049 "tRNA binding" evidence=ISO

GO:0003723 "RNA binding" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA;ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=ISO

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA;ISO

GO:0043039 "tRNA aminoacylation" evidence=ISO

GO:0070184 "mitochondrial tyrosyl-tRNA aminoacylation" evidence=ISO

GO:0072545 "tyrosine binding" evidence=IEA;ISO

UNIPROTKB|I3L635 LOC100624597 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 84/205 (40%), Positives = 128/205 (62%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             +VTG+   G++ P+I S +G K GKSA NA+WL+ + +S FELYQ+ +R +D+ V   LK
Sbjct:   218 KVTGEDVFGISVPLITSTTGAKLGKSAGNAVWLNREKTSPFELYQFFVRLQDNLVERYLK 277

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + +  +PE+R  QK+LA ++T LVHG+EGL SAK  TQALY   +D
Sbjct:   278 LFTFLPLPEIDHIMQLHVKEPEKRGPQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSID 337

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   EL+++PG S+L+        P        I+EGG  +N++
Sbjct:   338 ALEVMSDQELKELFKEASFSELVLDPGTSVLDTCRKANAIPDGPRGYRMITEGGVSINHR 397

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   398 QVTNPESVLVVGQHILKNGLSLLKI 422

GO:0005524 "ATP binding" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

MGI|MGI:1917370 Yars2 "tyrosyl-tRNA synthetase 2 (mitochondrial)" [Mus musculus (taxid:10090)]

 Score = 407 (148.3 bits), Expect = 5.5e-38, P = 5.5e-38
 Identities = 83/205 (40%), Positives = 128/205 (62%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             ++TG+   G+T P+I S +G K GKSA NA+WL+ + +S FELYQ+ +R +D  V   LK
Sbjct:   255 KLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNREKTSPFELYQFFVRQQDDSVERYLK 314

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + +  +PE+R AQK+LA ++T LVHG+EGL SAK  TQALY   ++
Sbjct:   315 LFTFLPLPEIDHIMQLHVKEPEKRVAQKRLAAEVTKLVHGQEGLDSAKRCTQALYHSSIE 374

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   EL+++PG S+++        P        I+EGG  +N++
Sbjct:   375 ALEVMSDQELKELFKEASFSELVLDPGTSVIDTCRKANAIPDGPRGYRMITEGGVSINHR 434

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   435 QVTNPESVLVIGQHILKNGLSLLKI 459

GO:0000049 "tRNA binding" evidence=ISO

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005739 "mitochondrion" evidence=IDA

GO:0006412 "translation" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0043039 "tRNA aminoacylation" evidence=ISO

GO:0070184 "mitochondrial tyrosyl-tRNA aminoacylation" evidence=ISO

GO:0072545 "tyrosine binding" evidence=ISO

UNIPROTKB|A5D7G0 YARS2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 400 (145.9 bits), Expect = 3.0e-37, P = 3.0e-37
 Identities = 83/205 (40%), Positives = 126/205 (61%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             ++TG+   G++ P+I S +G K GKSA NA+WL+   +S FELYQ+ +R +D  V   LK
Sbjct:   261 KLTGEDVFGISVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFLRQQDDLVERYLK 320

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + +  +PE+R  QK+LA ++T LVHG+EGL SAK  TQALY   +D
Sbjct:   321 LFTFLPLPEIDHIMQLHVKEPEKRGPQKRLAAEVTKLVHGQEGLASAKRCTQALYHSSID 380

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   EL+++PG S+L+        P        I+EGG  +N++
Sbjct:   381 ALEVMSDQELKELFKEASFSELVLDPGTSVLDTCRKANAIPDGPRGYRMITEGGVSINHR 440

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   441 QVTNPESVLVVGQHILKNGLSLLKI 465

GO:0072545 "tyrosine binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|Q9Y2Z4 YARS2 "Tyrosine--tRNA ligase, mitochondrial" [Homo sapiens (taxid:9606)]

 Score = 396 (144.5 bits), Expect = 8.0e-37, P = 8.0e-37
 Identities = 83/205 (40%), Positives = 121/205 (59%)

Query:     2 EVTGDG--GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK 59
             ++TG+   G+T P+I S +G K GKSA NA+WL+   +S FELYQ+ +R  D  V   LK
Sbjct:   260 KLTGEDVFGITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLK 319

Query:    60 LFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
             LF+F  L  I+   + +  +PE R  QK+LA ++T LVHG EGL SAK  TQALY   +D
Sbjct:   320 LFTFLPLPEIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQALYHSSID 379

Query:   120 SLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYK 179
             +L  ++  +   +F  A   E  ++PG S+L+        P        I+EGG  +N++
Sbjct:   380 ALEVMSDQELKELFKEAPFSEFFLDPGTSVLDTCRKANAIPDGPRGYRMITEGGVSINHQ 439

Query:   180 KVQNPQEVLSPSAHILPNSLTLLRV 204
             +V NP+ VL    HIL N L+LL++
Sbjct:   440 QVTNPESVLIVGQHILKNGLSLLKI 464

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IDA;NAS;TAS

GO:0005739 "mitochondrion" evidence=IC;NAS;TAS

GO:0006412 "translation" evidence=NAS

GO:0005759 "mitochondrial matrix" evidence=TAS

GO:0006418 "tRNA aminoacylation for protein translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0000049 "tRNA binding" evidence=IDA;TAS

GO:0005524 "ATP binding" evidence=TAS

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0043039 "tRNA aminoacylation" evidence=IDA

GO:0070184 "mitochondrial tyrosyl-tRNA aminoacylation" evidence=IC;IMP

GO:0072545 "tyrosine binding" evidence=IDA

ZFIN|ZDB-GENE-030131-6268 yars2 "tyrosyl-tRNA synthetase 2, mitochondrial" [Danio rerio (taxid:7955)]

 Score = 395 (144.1 bits), Expect = 1.0e-36, P = 1.0e-36
 Identities = 77/197 (39%), Positives = 120/197 (60%)

Query:     8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
             GLT P++ +  G+K GK+A NA+WL+   +S FE YQY +R  D+ V   LKLF+F SL+
Sbjct:   265 GLTVPLVTTSMGDKLGKTAGNAVWLNRDKTSPFEFYQYFLRLPDNSVERYLKLFTFLSLS 324

Query:    68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
              +E+   Q    P +R A K+LA ++T LVHG++GL+SAK  T ALY   +++L  ++ T
Sbjct:   325 EVENLMEQQRKDPGKRIAHKRLAAEVTKLVHGKDGLESAKRCTTALYHSSIEALEQMSDT 384

Query:   128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
             +   IF  A   E  +EPG ++L+     +  P        I +GG ++N+++ +NP++V
Sbjct:   385 ELQEIFREAPFHEFFLEPGTTVLDACRRARAIPDGPRGYQMIKDGGVWINHQRAENPEQV 444

Query:   188 LSPSAHILPNSLTLLRV 204
             L     IL N L+L+RV
Sbjct:   445 LIVGQQILSNGLSLIRV 461

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

GO:0006412 "translation" evidence=IEA

UNIPROTKB|E1C266 YARS2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 386 (140.9 bits), Expect = 9.2e-36, P = 9.2e-36
 Identities = 79/197 (40%), Positives = 120/197 (60%)

Query:     8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
             G+T P+I S +G+K GK+A NA+WL+   +S FELYQ+ +R +D  V   LKLF+F  L 
Sbjct:   275 GITVPLITSTTGDKLGKTAGNAVWLNRDKTSPFELYQFFVRQQDDIVEKYLKLFTFLPLE 334

Query:    68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
              I+     +  +PE+   QK+LA ++T LVHG EGL+SAK  T+ALY   +++L +++  
Sbjct:   335 EIDHIMEMHAREPEKWGPQKRLAAEVTKLVHGREGLESAKRCTKALYHSSVEALEAMSDQ 394

Query:   128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
             +   +F  A   EL++EPG ++L+L       P        I++GG  VN  +V NP+ V
Sbjct:   395 ELQELFRQAPSAELILEPGTTLLDLCRKANAIPHGPSGYQKITDGGVSVNGIRVTNPETV 454

Query:   188 LSPSAHILPNSLTLLRV 204
             L    HIL N ++LLR+
Sbjct:   455 LILGQHILKNGVSLLRI 471

GO:0003723 "RNA binding" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0072545 "tyrosine binding" evidence=IEA

UNIPROTKB|P0AGJ9 tyrS "tyrosyl-tRNA synthetase" [Escherichia coli K-12 (taxid:83333)]

 Score = 299 (110.3 bits), Expect = 1.5e-26, P = 1.5e-26
 Identities = 70/197 (35%), Positives = 110/197 (55%)

Query:     8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
             GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct:   222 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 281

Query:    68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
              I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK  T+ L+S    SL +L+  
Sbjct:   282 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAKRITECLFS---GSLSALSEA 338

Query:   128 DASRIFP-GARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQE 186
             D  ++   G  +VE  ME G  +++  + ++  P   +A  TI+     +N +K  +P+ 
Sbjct:   339 DFEQLAQDGVPMVE--MEKGADLMQALVDSELQPSRGQARKTIASNAITINGEKQSDPEY 396

Query:   187 VLSPSAHILPNSLTLLR 203
                    +     TLLR
Sbjct:   397 FFKEEDRLF-GRFTLLR 412

GO:0006437 "tyrosyl-tRNA aminoacylation" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0016020 "membrane" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0016874 "ligase activity" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004831 "tyrosine-tRNA ligase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9W107	SYYM_DROME	6, ., 1, ., 1, ., 1	0.5279	0.8174	0.4245	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	6.1.1.1	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	241
PRK05912	408	PRK05912, PRK05912, tyrosyl-tRNA synthetase; Valid	1e-41
COG0162	401	COG0162, TyrS, Tyrosyl-tRNA synthetase [Translatio	3e-34
PRK13354	410	PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provi	7e-34
TIGR00234	377	TIGR00234, tyrS, tyrosyl-tRNA synthetase	2e-22
cd00805	269	cd00805, TyrRS_core, catalytic core domain of tyro	4e-22
pfam00579	291	pfam00579, tRNA-synt_1b, tRNA synthetases class I	2e-16
cd00395	273	cd00395, Tyr_Trp_RS_core, catalytic core domain of	3e-15

>gnl|CDD|235645 PRK05912, PRK05912, tyrosyl-tRNA synthetase; Validated

 Score =  146 bits (371), Expect = 1e-41
 Identities = 69/197 (35%), Positives = 103/197 (52%), Gaps = 17/197 (8%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G+K GKS  NA+WLD + +S +E+YQ  +   D++V+  LKL +F SL 
Sbjct: 219 GLTMPLLTGLDGKKMGKSEGNAVWLDEEKTSPYEMYQKWMNISDADVWRYLKLLTFLSLE 278

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE+ + +    P  R A+K LAE++T LVHGEE  ++A+ A +AL+       G L   
Sbjct: 279 EIEELEEELAEGPNPREAKKVLAEEITALVHGEEAAEAAEEAFEALFGS-----GELPD- 332

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
                      VEL  E G+ +L L +     P   EA   I +GG  +N +KV +   V
Sbjct: 333 -------DLPEVEL--ELGIDLLALLVEAGLVPSKSEARRLIKQGGVKINGEKVSDENYV 383

Query: 188 LSPSAHILPNSLTLLRV 204
           L  +A       T+L+ 
Sbjct: 384 L--TADDRFGKYTVLQR 398

Length = 408

>gnl|CDD|223240 COG0162, TyrS, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

 Score =  126 bits (318), Expect = 3e-34
 Identities = 71/197 (36%), Positives = 110/197 (55%), Gaps = 17/197 (8%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLTTP++    G+K GKS   A+WLDS+ +S ++ YQY +  +D++V   LKL +F SL 
Sbjct: 211 GLTTPLLTGLDGKKMGKSEGGAVWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLE 270

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE+ ++     PE R A+K LA+++T LVHGEE  ++A+   + L+S+ L    +L   
Sbjct: 271 EIEEIEKYVLKGPEPREAKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEGLPE--NLPPA 328

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           D  +      +V+LL       ++  LA    P   EA   I +GG  +N +KV++   V
Sbjct: 329 DLKQKLE-DGLVDLL-------VDAGLA----PSRSEARRLIQQGGVKINGEKVEDENYV 376

Query: 188 LSPSAHILPNSLTLLRV 204
           LS    +L N L +LR 
Sbjct: 377 LS---DLLDNGLLVLRR 390

Length = 401

>gnl|CDD|237360 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional

 Score =  125 bits (316), Expect = 7e-34
 Identities = 63/187 (33%), Positives = 98/187 (52%), Gaps = 13/187 (6%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++E   G K GKSA  AIWLD + +S +E YQ+ +   D +V   LKLF+  S  
Sbjct: 217 GLTMPLLEGADGTKMGKSAGGAIWLDPEKTSPYEFYQFWMNIDDRDVVKYLKLFTDLSPD 276

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I++ + Q E +P  R A+K LAE++T  VHGEE  + A+   +AL+S D+  L  +   
Sbjct: 277 EIDELEAQLETEPNPRDAKKVLAEEITKFVHGEEAAEEAEKIFKALFSGDVKPLKDIPTF 336

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           + S       +V+LL++ G+            P  +EA   I  G   +N +KV +   +
Sbjct: 337 EVSA--ETKNLVDLLVDLGLE-----------PSKREARRLIQNGAIKINGEKVTDVDAI 383

Query: 188 LSPSAHI 194
           ++P    
Sbjct: 384 INPEDAF 390

Length = 410

>gnl|CDD|232889 TIGR00234, tyrS, tyrosyl-tRNA synthetase

 Score = 94.0 bits (234), Expect = 2e-22
 Identities = 58/182 (31%), Positives = 87/182 (47%), Gaps = 17/182 (9%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    GEK GKS   A+ LD      ++ YQ+ I T D +V  +LKLF+F  L 
Sbjct: 208 GLTVPLLTPADGEKMGKSEGGAVSLDEGK---YDFYQFWINTPDEDVKKILKLFTFLGLE 264

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE         P  R  ++ LA+++T  VHGEE   +A+  ++AL+S  L+        
Sbjct: 265 EIEALV--ELKGPSPREVKENLAKEITKYVHGEEAALAAEEISEALFSGGLNPDE----L 318

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
              R       + L       +L LS     FP   EA   I +GG Y+N +KV++ + +
Sbjct: 319 PIFRPEKFGGDITL-----ADLLVLSGL---FPSKSEARRDIKQGGVYINGEKVKDLEPI 370

Query: 188 LS 189
             
Sbjct: 371 RK 372

This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples [Protein synthesis, tRNA aminoacylation]. Length = 377

>gnl|CDD|173902 cd00805, TyrRS_core, catalytic core domain of tyrosinyl-tRNA synthetase

 Score = 91.1 bits (227), Expect = 4e-22
 Identities = 37/89 (41%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLTTP++    G K  KS  NAIW D  L S +++YQ +    D +V + LKLF+F    
Sbjct: 182 GLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKLFTFLDYE 240

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLL 96
            IE+ + ++   P  R A+K LAE+LT L
Sbjct: 241 EIEELEEEHAEGPLPRDAKKALAEELTKL 269

Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. Length = 269

>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y)

 Score = 76.2 bits (188), Expect = 2e-16
 Identities = 41/110 (37%), Positives = 56/110 (50%), Gaps = 3/110 (2%)

Query: 8   GLTTPIIESESGE-KFGKSARN-AIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDS 65
           GLT P++    G  K  KSA N AI+LD +  S ++  Q      D EV   LKLF+  S
Sbjct: 183 GLTNPLLTGLDGGKKMSKSAGNSAIFLDDEKESVYKKIQKAYTDPDREVRKDLKLFTELS 242

Query: 66  LAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYS 115
              IE  +      P +R A++ LA ++T LVHG +  K+A  A  AL  
Sbjct: 243 NEEIEILEAFLGKGP-KREAEELLAREVTGLVHGGDLKKAAAEAVNALLE 291

Length = 291

>gnl|CDD|173893 cd00395, Tyr_Trp_RS_core, catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase

 Score = 72.7 bits (178), Expect = 3e-15
 Identities = 37/87 (42%), Positives = 53/87 (60%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGKS     WLD++ +S +E YQ+ I   DS+V ++LK F+F S  
Sbjct: 185 GLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKYFTFLSKE 244

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLT 94
            IE  +++    P  R AQK LAE++T
Sbjct: 245 EIERLEQEQYEAPGYRVAQKTLAEEVT 271

Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. Length = 273

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	241
KOG2623|consensus	467		100.0
PRK13354	410	tyrosyl-tRNA synthetase; Provisional	100.0
PRK05912	408	tyrosyl-tRNA synthetase; Validated	100.0
COG0162	401	TyrS Tyrosyl-tRNA synthetase [Translation, ribosom	100.0
TIGR00234	377	tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA sy	100.0
cd00395	273	Tyr_Trp_RS_core catalytic core domain of tyrosinyl	99.86
cd00805	269	TyrRS_core catalytic core domain of tyrosinyl-tRNA	99.81
PF00579	292	tRNA-synt_1b: tRNA synthetases class I (W and Y);	99.52
PLN02486	383	aminoacyl-tRNA ligase	99.42
PTZ00126	383	tyrosyl-tRNA synthetase; Provisional	99.41
cd00806	280	TrpRS_core catalytic core domain of tryptophanyl-t	99.39
PRK08560	329	tyrosyl-tRNA synthetase; Validated	99.36
PRK12284	431	tryptophanyl-tRNA synthetase; Reviewed	99.34
PRK12285	368	tryptophanyl-tRNA synthetase; Reviewed	99.33
PRK12556	332	tryptophanyl-tRNA synthetase; Provisional	99.3
PRK00927	333	tryptophanyl-tRNA synthetase; Reviewed	99.29
PRK12282	333	tryptophanyl-tRNA synthetase II; Reviewed	99.28
PRK12283	398	tryptophanyl-tRNA synthetase; Reviewed	99.27
TIGR00233	328	trpS tryptophanyl-tRNA synthetase. This model repr	99.23
COG0180	314	TrpS Tryptophanyl-tRNA synthetase [Translation, ri	99.13
PTZ00348	682	tyrosyl-tRNA synthetase; Provisional	99.06
PF01479	48	S4: S4 domain; InterPro: IPR002942 Ribosomes are t	98.82
PLN02886	389	aminoacyl-tRNA ligase	98.78
KOG2144|consensus	360		98.18
PF13275	65	S4_2: S4 domain; PDB: 1P9K_A.	97.99
PRK11507	70	ribosome-associated protein; Provisional	97.91
KOG2713|consensus	347		97.9
cd00165	70	S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The	97.9
PRK04051	177	rps4p 30S ribosomal protein S4P; Validated	97.86
smart00363	60	S4 S4 RNA-binding domain.	97.77
TIGR02988	59	YaaA_near_RecF S4 domain protein YaaA. This small	97.76
PRK10348	133	ribosome-associated heat shock protein Hsp15; Prov	97.6
TIGR01018	162	rpsD_arch ribosomal protein S4(archaeal type)/S9(e	97.58
PTZ00348	682	tyrosyl-tRNA synthetase; Provisional	97.33
COG1187	248	RsuA 16S rRNA uridine-516 pseudouridylate synthase	97.32
COG1189	245	Predicted rRNA methylase [Translation, ribosomal s	97.26
COG2501	73	S4-like RNA binding protein [Replication, recombin	97.1
TIGR01017	200	rpsD_bact ribosomal protein S4, bacterial/organell	97.05
COG0522	205	RpsD Ribosomal protein S4 and related proteins [Tr	97.02
KOG2145|consensus	397		96.99
TIGR00478	228	tly hemolysin TlyA family protein. Hemolysins are	96.95
CHL00113	201	rps4 ribosomal protein S4; Reviewed	96.94
COG1188	100	Ribosome-associated heat shock protein implicated	96.89
PTZ00155	181	40S ribosomal protein S9; Provisional	96.78
PRK05327	203	rpsD 30S ribosomal protein S4; Validated	96.68
PLN00189	194	40S ribosomal protein S9; Provisional	96.37
TIGR03069	257	PS_II_S4 photosystem II S4 domain protein. Members	96.16
PRK10700	289	23S rRNA pseudouridylate synthase B; Provisional	95.97
cd00818	338	IleRS_core catalytic core domain of isoleucyl-tRNA	95.95
PRK10475	290	23S rRNA pseudouridine synthase F; Provisional	95.86
PRK00750	510	lysK lysyl-tRNA synthetase; Reviewed	95.31
PLN00051	267	RNA-binding S4 domain-containing protein; Provisio	95.21
cd00668	312	Ile_Leu_Val_MetRS_core catalytic core domain of is	94.87
COG2302	257	Uncharacterized conserved protein, contains S4-lik	94.8
PRK12418	384	cysteinyl-tRNA synthetase; Provisional	94.71
COG0060	933	IleS Isoleucyl-tRNA synthetase [Translation, ribos	94.69
cd00812	314	LeuRS_core catalytic core domain of leucyl-tRNA sy	94.63
cd00817	382	ValRS_core catalytic core domain of valyl-tRNA syn	94.55
PF00133	601	tRNA-synt_1: tRNA synthetases class I (I, L, M and	94.5
PRK11893	511	methionyl-tRNA synthetase; Reviewed	94.36
PTZ00427	1205	isoleucine-tRNA ligase, putative; Provisional	94.23
PLN02381	1066	valyl-tRNA synthetase	94.22
PLN02882	1159	aminoacyl-tRNA ligase	94.14
PRK05743	912	ileS isoleucyl-tRNA synthetase; Reviewed	94.13
PRK05729	874	valS valyl-tRNA synthetase; Reviewed	94.07
PRK14900	1052	valS valyl-tRNA synthetase; Provisional	93.97
PRK13208	800	valS valyl-tRNA synthetase; Reviewed	93.89
TIGR03447	411	mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-	93.89
COG0525	877	ValS Valyl-tRNA synthetase [Translation, ribosomal	93.83
COG0215	464	CysS Cysteinyl-tRNA synthetase [Translation, ribos	93.79
PRK06039	975	ileS isoleucyl-tRNA synthetase; Reviewed	93.74
PRK11180	325	rluD 23S rRNA pseudouridine synthase D; Provisiona	93.73
PRK13804	961	ileS isoleucyl-tRNA synthetase; Provisional	93.66
PTZ00419	995	valyl-tRNA synthetase-like protein; Provisional	93.65
PF01406	300	tRNA-synt_1e: tRNA synthetases class I (C) catalyt	93.62
PRK04313	237	30S ribosomal protein S4e; Validated	93.47
TIGR00422	861	valS valyl-tRNA synthetase. The valyl-tRNA synthet	93.35
TIGR00392	861	ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA	93.32
PLN02943	958	aminoacyl-tRNA ligase	93.29
cd00672	213	CysRS_core catalytic core domain of cysteinyl tRNA	93.23
PRK12300	897	leuS leucyl-tRNA synthetase; Reviewed	92.98
PRK12268	556	methionyl-tRNA synthetase; Reviewed	92.85
PRK00133	673	metG methionyl-tRNA synthetase; Reviewed	92.84
PLN02843	974	isoleucyl-tRNA synthetase	92.84
TIGR00005	299	rluA_subfam pseudouridine synthase, RluA family. m	92.81
cd00814	319	MetRS_core catalytic core domain of methioninyl-tR	92.79
PF09334	391	tRNA-synt_1g: tRNA synthetases class I (M); InterP	92.67
PRK10839	232	16S rRNA pseudouridylate synthase A; Provisional	92.66
KOG0432|consensus	995		92.52
PTZ00223	273	40S ribosomal protein S4; Provisional	92.32
PLN02610	801	probable methionyl-tRNA synthetase	92.27
TIGR00395	938	leuS_arch leucyl-tRNA synthetase, archaeal and cyt	92.26
COG0143	558	MetG Methionyl-tRNA synthetase [Translation, ribos	92.26
PRK00260	463	cysS cysteinyl-tRNA synthetase; Validated	92.26
PLN02224	616	methionine-tRNA ligase	92.1
PRK14535	699	cysS cysteinyl-tRNA synthetase; Provisional	92.06
TIGR00435	465	cysS cysteinyl-tRNA synthetase. This model finds t	91.99
PLN02946	557	cysteine-tRNA ligase	91.68
cd00418	230	GlxRS_core catalytic core domain of glutamyl-tRNA	91.57
PTZ00118	262	40S ribosomal protein S4; Provisional	91.37
TIGR00398	530	metG methionyl-tRNA synthetase. The methionyl-tRNA	91.21
PRK12267	648	methionyl-tRNA synthetase; Reviewed	91.15
PLN00036	261	40S ribosomal protein S4; Provisional	91.13
KOG0437|consensus	1080		90.96
cd00674	353	LysRS_core_class_I catalytic core domain of class	90.9
PLN02959	1084	aminoacyl-tRNA ligase	90.63
PRK14536	490	cysS cysteinyl-tRNA synthetase; Provisional	90.48
KOG4655|consensus	181		90.39
PRK11025	317	23S rRNA pseudouridylate synthase C; Provisional	90.16
KOG0436|consensus	578		90.04
PTZ00399	651	cysteinyl-tRNA-synthetase; Provisional	90.03
PRK01611	507	argS arginyl-tRNA synthetase; Reviewed	90.0
cd00808	239	GluRS_core catalytic core domain of discriminating	89.93
PRK14534	481	cysS cysteinyl-tRNA synthetase; Provisional	89.68
COG0564	289	RluA Pseudouridylate synthases, 23S RNA-specific [	87.29
KOG2007|consensus	586		85.76
PF01921	360	tRNA-synt_1f: tRNA synthetases class I (K); InterP	85.74
KOG3301|consensus	183		85.58
COG0495	814	LeuS Leucyl-tRNA synthetase [Translation, ribosoma	85.04
TIGR00467	515	lysS_arch lysyl-tRNA synthetase, archaeal and spir	84.78
PLN02563	963	aminoacyl-tRNA ligase	84.4
KOG0433|consensus	937		82.56
TIGR00396	842	leuS_bact leucyl-tRNA synthetase, eubacterial and	80.05

>KOG2623|consensus

Probab=100.00  E-value=8e-54  Score=392.59  Aligned_cols=212  Identities=36%  Similarity=0.570  Sum_probs=199.0

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ++.+||+|+||||+++|.|+|||+|||||||+++||||++||||.++||++|++||++|||+|.+||++++++|.+.|.+
T Consensus       255 ~~~vfGlT~PLlTsstG~KlGKSaGnAvWLdp~~tspy~lYQfF~~~pDd~v~k~LklfTfl~l~eI~~I~~~H~k~P~~  334 (467)
T KOG2623|consen  255 QAFVFGLTFPLLTSSTGAKLGKSAGNAVWLDPSKTSPYHLYQFFASLPDDDVEKFLKLFTFLPLEEIKQILEEHRKEPSQ  334 (467)
T ss_pred             ccceeeeeeeeEecCcchhhccCCCceEEecCccCCcHHHHHHHHhCchhHHHHHHHHHhcCCHHHHHHHHHHHhcChhh
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD  162 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk  162 (241)
                      |.+|+.||+|||.+|||+++++.|+++|++||++....+..++..++.++|+++|...+..++++++.+++++++.++|+
T Consensus       335 r~aQ~~LA~eVTr~VHG~egL~~A~r~T~al~g~~~~~~~~ls~~ei~~lfk~a~~~~l~~~~~~s~~~l~~ka~~~~s~  414 (467)
T KOG2623|consen  335 RIAQKLLAAEVTRMVHGKEGLEVAERCTKALFGAKKAGLSGLSLSEILQLFKDATFIDLKDEPGVSILDLLRKASRFPSG  414 (467)
T ss_pred             hhHHHHHHHHHHHHHcccchHHHHHHHHHHhhcccccccccCCHHHHHHHHhcCCceecccCCCCcHHHHHHHhhcCCCc
Confidence            99999999999999999999999999999999997777889999999999999999888766799999999999999999


Q ss_pred             HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCC-eEEEEeccccEEEEEEc
Q psy938          163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNS-LTLLRVEVSANIIAKSA  215 (241)
Q Consensus       163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~-~~llr~GKk~~~~i~~~  215 (241)
                      +||||+|+|||||+|++++++++.. ..+.++++++ +.+||+|||+|++|+|.
T Consensus       415 ~~a~r~i~qG~vslnh~~v~~es~~-~~~~~i~~nr~L~lLr~GKrnf~ivr~~  467 (467)
T KOG2623|consen  415 KEARRMIQQGGVSLNHEKVRDESVS-IAGPFILNNRGLSLLRAGKRNFVIVRWV  467 (467)
T ss_pred             HHHHHHHHccceeecCccccCchhh-ccccceecCCCeEEEEecCcceEEEEeC
Confidence            9999999999999999999995543 3345888884 55999999999999984

>PRK13354 tyrosyl-tRNA synthetase; Provisional

Probab=100.00  E-value=4.8e-50  Score=377.90  Aligned_cols=200  Identities=32%  Similarity=0.496  Sum_probs=181.8

Q ss_pred             CCCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938            2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE   81 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~   81 (241)
                      +...+|++|+|||+|+||.|||||.||+|||++++||||++||||++++|++|.+|+++||+++.++|+++++.|..+++
T Consensus       211 ~~~~~~~lt~PlL~g~dG~KMsKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~~~t~l~~~ei~~l~~~~~~~~~  290 (410)
T PRK13354        211 EGEEQFGLTMPLLEGADGTKMGKSAGGAIWLDPEKTSPYEFYQFWMNIDDRDVVKYLKLFTDLSPDEIDELEAQLETEPN  290 (410)
T ss_pred             CCCCceEeccCCccCCCCCccCCCCCCceeccCCCCCHHHHHHHHHcCChHHHHHHHHHHhCCCHHHHHHHHHHHhcCCC
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCC
Q psy938           82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPR  161 (241)
Q Consensus        82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~S  161 (241)
                      ++++|+.||++|++++||.+++++|+++++++|+++...   +  .       ++|.+++. ..+.++.++|+.+|+++|
T Consensus       291 ~~~~Kk~LA~~v~~~vhg~~~~~~a~~~~~~~f~~~~~~---~--~-------~~p~~~~~-~~~~~~~~~l~~~~~~~S  357 (410)
T PRK13354        291 PRDAKKVLAEEITKFVHGEEAAEEAEKIFKALFSGDVKP---L--K-------DIPTFEVS-AETKNLVDLLVDLGLEPS  357 (410)
T ss_pred             hHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhCCCCCC---c--C-------CCCeEEec-CCCCCHHHHHHHhCCCCC
Confidence            999999999999999999999999999999999865211   1  1       45665553 236789999999999999


Q ss_pred             HHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEc
Q psy938          162 DKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSA  215 (241)
Q Consensus       162 ksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~  215 (241)
                      ++||||+|+||||+|||++++|+++.+... +++++++++||+|||+|++|+|.
T Consensus       358 ~~earrli~~ggv~in~~~v~~~~~~~~~~-~~l~~~~~~lr~GKk~~~~i~~~  410 (410)
T PRK13354        358 KREARRLIQNGAIKINGEKVTDVDAIINPE-DAFDGKFVILRRGKKKFFLVKLK  410 (410)
T ss_pred             HHHHHHHHHcCCEEECCEEccCcccccChh-hhcCCCEEEEEeCCccEEEEEEC
Confidence            999999999999999999999999888765 68899999999999999999873

>PRK05912 tyrosyl-tRNA synthetase; Validated

Probab=100.00  E-value=1.4e-48  Score=367.81  Aligned_cols=195  Identities=34%  Similarity=0.487  Sum_probs=177.9

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..++|++|+|||||+||+|||||.||+|||+++||||+++||||+|++|++|++|+++||+++.++|++++++|..++++
T Consensus       214 ~~~~~~l~~plL~~~~G~KMsKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~~~t~~~~~ei~~l~~~~~~g~~~  293 (408)
T PRK05912        214 GKPQFGLTMPLLTGLDGKKMGKSEGNAVWLDEEKTSPYEMYQKWMNISDADVWRYLKLLTFLSLEEIEELEEELAEGPNP  293 (408)
T ss_pred             CCCeEEEecCCcCCCCCCcccCCCCCceeCCCCCCCHHHHHHHHhcCChHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCh
Confidence            34789999999999999999999999999999999999999999999999999999999999999999999999888899


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD  162 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk  162 (241)
                      +++|+.||++|++++||++++++|+++++++|+++.     ++        .++|.+++.  .+.++.++|+.+|+++|+
T Consensus       294 ~~~Kk~LA~~v~~~lhg~~~~~~a~~~~~~~f~~~~-----~~--------~~~~~~~~~--~~~~~~~~l~~~~~~~S~  358 (408)
T PRK05912        294 REAKKVLAEEITALVHGEEAAEAAEEAFEALFGSGE-----LP--------DDLPEVELE--LGIDLLALLVEAGLVPSK  358 (408)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhcCCC-----Cc--------cCCCeEEec--CCCcHHHHHHHhCCCCCH
Confidence            999999999999999999999999999999998641     11        135555552  267899999999999999


Q ss_pred             HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEE
Q psy938          163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKS  214 (241)
Q Consensus       163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~  214 (241)
                      +||||+|+||||+|||++|+|++..+... ++ ++++++||+|||+|++|+|
T Consensus       359 ~earr~i~~g~v~in~~~v~~~~~~~~~~-~~-~~~~~~lr~GKk~~~~i~~  408 (408)
T PRK05912        359 SEARRLIKQGGVKINGEKVSDENYVLTAD-DR-FGKYTVLQRGKKKFARVTL  408 (408)
T ss_pred             HHHHHHHHcCCEEECCEEecCcccccccc-cc-CCCEEEEEeCCCceEEEeC
Confidence            99999999999999999999998888754 56 8889999999999999975

>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=3.3e-44  Score=335.90  Aligned_cols=198  Identities=33%  Similarity=0.507  Sum_probs=181.7

Q ss_pred             CCCCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938            1 MEVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKP   80 (241)
Q Consensus         1 ~~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~   80 (241)
                      +++.++||+|+|||+|+||.|||||+||++|+++++||||+|||||+|++|.++.+|+.+||+++.++|.++++.+..++
T Consensus       204 ~g~~~~~~lt~PLL~~ldG~KmgKs~~~a~~~~s~~~Sp~~~yq~~~~i~D~~~~~~~~~~t~l~~~eI~~i~~~~~~~~  283 (401)
T COG0162         204 LGQKKVVGLTTPLLTGLDGKKMGKSEGGAVWLDSEKTSPYDFYQYWMNIEDADVKRFLKLLTFLSLEEIEEIEKYVLKGP  283 (401)
T ss_pred             hCCCCeEEEEeccccCCCCCcccccCCCceEccCCCCCcHhhhhcHhcCcHHHHHHHHHHhCcCChHHHHHHHHHhhcCC
Confidence            35678999999999999999999999999999999999999999999999999999999999998899999999888888


Q ss_pred             ChHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCC
Q psy938           81 EERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFP  160 (241)
Q Consensus        81 ~~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~  160 (241)
                      +++.+|+.||.++|..+||++++.+|.+.++.+|.++  ..+++++.++..        .+    ..+++++|+.+|+++
T Consensus       284 ~~r~~k~~LA~e~~~~~hG~~~a~~a~~~~~~~F~~g--~~~~l~~~dlk~--------~~----~~~~~~~lv~~~L~p  349 (401)
T COG0162         284 EPREAKKLLAKEVTKLVHGEEAAEAAEEEFEKLFSEG--LPENLPPADLKQ--------KL----EDGLVDLLVDAGLAP  349 (401)
T ss_pred             ChHHHHHHHHHHhhHhhcCHHHHHHHHHHHHHHHhcC--CcccCCHHHHhh--------hh----HHHHHHHHHHhCCcc
Confidence            9999999999999999999999999999999999986  345777777765        11    126899999999999


Q ss_pred             CHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEc
Q psy938          161 RDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSA  215 (241)
Q Consensus       161 SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~  215 (241)
                      |++||||+|++|||++||++++|++..+   .+++++++.+||+|||+|++|.+.
T Consensus       350 sr~earr~i~~g~v~in~~~v~d~~~~~---~~~~~~~~~~l~~GKkk~~~i~~~  401 (401)
T COG0162         350 SRSEARRLIQQGGVKINGEKVEDENYVL---SDLLDNGLLVLRRGKKKFALIVLK  401 (401)
T ss_pred             cHHHHHhhcccCCEEECCEeccccccch---hhccCCceEEEecccccEEEEeeC
Confidence            9999999999999999999999998777   367888999999999999999874

>TIGR00234 tyrS tyrosyl-tRNA synthetase

Probab=100.00  E-value=9.8e-34  Score=264.76  Aligned_cols=169  Identities=32%  Similarity=0.496  Sum_probs=149.9

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ...+|++|+|||+++||.|||||.||+|||++   +||++||||++.+|..+.+|+++||+++.+||+++++  ..++++
T Consensus       203 ~~~~~~~t~pLl~~~dg~KmgKS~~~~i~l~~---~~~~~~i~~~d~~D~~~~Ki~k~~t~~~~~ei~~l~~--~~~~~~  277 (377)
T TIGR00234       203 PSLGFGLTVPLLTPADGEKMGKSGGGAVSLDE---GKYDFYQFWINTPDEDVKKILKLFTFLGLEEIEALVE--LKGPSP  277 (377)
T ss_pred             CCCceeeceeeecCCCCCCccCCCCCcccCCc---cHhhhhhhhcCCcHHHHHHHHHHcCCCcHHHHHHHHH--hcccCH
Confidence            35689999999999999999999999999999   8899999999999999999999999999999999976  466899


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCC-CCcHHHHHHhcCCCCC
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEP-GMSMLELSLATKCFPR  161 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~-~~~l~~lLv~~gl~~S  161 (241)
                      +.+|+.||.+||+++||++++++|+++++.+|+++.     +        ..++|...+.... +.++.++++.+|+++|
T Consensus       278 ~~~q~~la~ei~~~vhg~~~~~~a~~~~~~~f~~~~-----~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~S  344 (377)
T TIGR00234       278 REVKENLAKEITKYVHGEEAALAAEEISEAIFSGGL-----N--------PDELPIFRPEKFGGDITLADLLVLSGLFPS  344 (377)
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCCC-----C--------ccCCCEEeecccCCCcCHHHHHHHcCCCcC
Confidence            999999999999999999999999999999998652     1        1234554443222 3789999999999999


Q ss_pred             HHHHHHHHHhCCeEEccEEecCCCCccC
Q psy938          162 DKEANLTISEGGFYVNYKKVQNPQEVLS  189 (241)
Q Consensus       162 ksEARRlI~qGgV~VNg~~v~d~~~~l~  189 (241)
                      +++|||+|++|||+||+.++++++.+..
T Consensus       345 ~~~arr~ik~g~v~vn~~~i~~~~~v~~  372 (377)
T TIGR00234       345 KSEARRDIKQGGVYINGEKVTDLEPIRK  372 (377)
T ss_pred             hHHHHHHHHhCCEEECCEeccCchhhhc
Confidence            9999999999999999999999877654

This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples.

>cd00395 Tyr_Trp_RS_core catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase

Probab=99.86  E-value=1.1e-21  Score=176.63  Aligned_cols=93  Identities=41%  Similarity=0.647  Sum_probs=88.8

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCChH
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEER   83 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~~   83 (241)
                      .++++++.|+|||++|.|||||.+|+|||++.++||+++||||+++.|++|.+|+++||+++.+||+++++++.++++++
T Consensus       181 ~~p~~l~~p~l~~l~G~KMSKS~~~~i~l~~~~dsp~~i~~ki~~a~d~~v~~~~~~~t~~~~~ei~~i~~~~~~~~~~~  260 (273)
T cd00395         181 TIAEGLTIPLVTKLDGPKFGKSESGPKWLDTEKTSPYEFYQFWINAVDSDVINILKYFTFLSKEEIERLEQEQYEAPGYR  260 (273)
T ss_pred             CCCeEEeeccccCCCCCcCCCCCCCCccccccCCCHHHHHHHHHcccHhHHHHHHHHHcCCCHHHHHHHHHHHhcCCCHH
Confidence            46899999999999999999999999999988889999999999999999999999999999999999999998888999


Q ss_pred             HHHHHHHHHHHhh
Q psy938           84 RAQKKLAEDLTLL   96 (241)
Q Consensus        84 ~~Kk~LA~~i~~~   96 (241)
                      ++|+.||++|+++
T Consensus       261 ~~K~~La~~i~~~  273 (273)
T cd00395         261 VAQKTLAEEVTKT  273 (273)
T ss_pred             HHHHHHHHHHHhC
Confidence            9999999999863

Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.

>cd00805 TyrRS_core catalytic core domain of tyrosinyl-tRNA synthetase

Probab=99.81  E-value=1.3e-19  Score=162.70  Aligned_cols=93  Identities=40%  Similarity=0.633  Sum_probs=87.0

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..++++++.|+|++++|+|||||.+|++| +.-.+||+++||||+++.|++|.+|+++|++++.+++++++++|..++.+
T Consensus       177 ~~~~~~l~~~ll~~l~G~KMSKS~~~~~~-i~l~dsp~~i~~Ki~~a~~~~v~~~l~~~~~~~~~~~eel~~~~~~~~~~  255 (269)
T cd00805         177 YKKVVGLTTPLLTGLDGGKMSKSEGNAIW-DPVLDSPYDVYQKIRNAFDPDVLEFLKLFTFLDYEEIEELEEEHAEGPLP  255 (269)
T ss_pred             CCCcEEEeeccccCCCCCcccCCCCCccc-ccCCCCHHHHHHHHHcCCcHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCH
Confidence            35789999999999999999999999998 77777999999999999999999999999999999999999999888779


Q ss_pred             HHHHHHHHHHHHhh
Q psy938           83 RRAQKKLAEDLTLL   96 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~   96 (241)
                      +++|+.||++|+++
T Consensus       256 ~~~K~~la~~i~~l  269 (269)
T cd00805         256 RDAKKALAEELTKL  269 (269)
T ss_pred             HHHHHHHHHHHHhC
Confidence            99999999999864

Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding.

>PF00579 tRNA-synt_1b: tRNA synthetases class I (W and Y); InterPro: IPR002305 The aminoacyl-tRNA synthetases (6

Probab=99.52  E-value=9.2e-15  Score=132.08  Aligned_cols=111  Identities=25%  Similarity=0.233  Sum_probs=92.9

Q ss_pred             CCceeeecccccCCCCC-ccccCCCC-eEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938            4 TGDGGLTTPIIESESGE-KFGKSARN-AIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE   81 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~-KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~   81 (241)
                      ..+++++.|+||++||. |||||.+| +|||+++.+++++.++++++.+|.++..++.+.++++.++++.++..+.+.+ 
T Consensus       180 ~~p~~l~~~~l~~l~G~~KMSKS~~ns~I~L~d~~~~i~~Ki~~a~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-  258 (292)
T PF00579_consen  180 PKPAGLTSPLLPGLDGQKKMSKSDPNSAIFLDDSPEEIRKKIKKAFCDPDRENPRLLKGRPFISPFLIERLEAFHGNDD-  258 (292)
T ss_dssp             SS-EEEEETCBBSTTSSSBTTTTTTGGS-BTTTTHHHHHHHHHHSHTSTTSHHHHHHHHHHTHHHHHHHHHHHHHHHHH-
T ss_pred             cCchheeeccccccCCccccCccCCccEEEEeccchhHHHHHHHHhhCCCcccccccccCCCCCHHHHHHHHHhcCCcc-
Confidence            47899999999999997 99999999 9999995555555555556668889999999999998888888887665444 


Q ss_pred             hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhcc
Q psy938           82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYS  115 (241)
Q Consensus        82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~  115 (241)
                      ++.+++.++++++..+|+.+..+++.++...+|+
T Consensus       259 ~~~~~~~~~~~~~g~l~~~~~K~~~~e~~~~~le  292 (292)
T PF00579_consen  259 YRSLEELLADYVSGELHPGDLKKALAEALNEFLE  292 (292)
T ss_dssp             ESHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHccCCcChHHHHHHHHHHHHHhhC
Confidence            6789999999999999999999999998888773

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2JAN_A 3P0J_B 3P0I_B 3P0H_B 1YID_C 2A4M_C 1YIA_C 1YI8_C 2EL7_A 3PRH_A ....

>PLN02486 aminoacyl-tRNA ligase

Probab=99.42  E-value=5.7e-13  Score=125.20  Aligned_cols=96  Identities=21%  Similarity=0.233  Sum_probs=78.6

Q ss_pred             eeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C---------------CChhHHHHHHHhcCC--C
Q psy938            7 GGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T---------------KDSEVYDLLKLFSFD--S   65 (241)
Q Consensus         7 ~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~---------------~D~~v~~~l~~~t~l--~   65 (241)
                      ..+..+.||+++|  .|||||.+| +|||++   +|+++++|+++ +               .|++++..+.||+++  +
T Consensus       249 ~~~~~~~lp~L~g~~~KMSkS~~nsaI~L~D---~p~~i~~KI~k~A~t~~~~t~~~~~~~gg~p~v~~~~~~l~~f~~d  325 (383)
T PLN02486        249 ALIESRFFPALQGESGKMSASDPNSAIYVTD---TPKEIKNKINKYAFSGGQDTVEEHRELGANLEVDIPWKYLNFFLED  325 (383)
T ss_pred             ceeccccccCCCCCCCcCcCcCCCCeeeccC---CHHHHHHHHhcCCCCCCCCcccccccCCCCCccchHHHHHHHHcCC
Confidence            3445678888887  699999987 799999   99999999999 3               256666666666666  3


Q ss_pred             HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHHHH
Q psy938           66 LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGLKS  105 (241)
Q Consensus        66 ~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a~~  105 (241)
                      .++++++.+.+..| .++.++|+.||+.|++++++-.+..+
T Consensus       326 d~~~eei~~~y~~G~l~~ge~K~~lae~i~~~l~~~qerr~  366 (383)
T PLN02486        326 DAELERIKKEYGSGRMLTGEVKKRLIEVLTEIVERHQRARA  366 (383)
T ss_pred             chHHHHHHHHhccCCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999766 68999999999999999999766543

>PTZ00126 tyrosyl-tRNA synthetase; Provisional

Probab=99.41  E-value=4.5e-13  Score=125.98  Aligned_cols=94  Identities=18%  Similarity=0.257  Sum_probs=80.0

Q ss_pred             CceeeecccccCC-CC-CccccCCCC-eEeecCCCCCHHHHHHHhhc-------CCChhHHHHHHHhcC-----------
Q psy938            5 GDGGLTTPIIESE-SG-EKFGKSARN-AIWLDSKLSSSFELYQYLIR-------TKDSEVYDLLKLFSF-----------   63 (241)
Q Consensus         5 ~~~~lt~pLL~g~-dG-~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-------~~D~~v~~~l~~~t~-----------   63 (241)
                      +++.++.|+|+|+ || +|||||.+| +|||++   +|+++++|+++       .+++.+..|+++++|           
T Consensus       239 ~~~~~~~~~lpgL~dg~~KMSKS~~ns~I~L~D---spe~I~kKI~kA~t~p~~~~~npv~~~~~~~~~~~~~~~~I~r~  315 (383)
T PTZ00126        239 KPIILSHHMLPGLLEGQEKMSKSDPNSAIFMED---SEEDVNRKIKKAYCPPGVIEGNPILAYFKSIVFPAFNSFTVLRK  315 (383)
T ss_pred             CceeecccccccCCCCCCCCCcCCCCCeecCCC---CHHHHHHHHHhCcCCCCCCCCCcchhhhhhcccccccceeEecc
Confidence            5677789999999 67 799999977 799999   99999999999       466789999998775           


Q ss_pred             ------CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938           64 ------DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        64 ------l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                            ++.++++++++.+..+ .+|.++|+.||+.|++++..-.
T Consensus       316 ~k~gg~~~~~~~eel~~~y~~g~l~p~dlK~~lae~i~~~L~PIR  360 (383)
T PTZ00126        316 EKNGGDVTYTTYEELEKDYLSGALHPGDLKPALAKYLNLMLQPVR  360 (383)
T ss_pred             ccccCccCcCCHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence                  1225789999998776 6999999999999999987543

>cd00806 TrpRS_core catalytic core domain of tryptophanyl-tRNA synthetase

Probab=99.39  E-value=1.6e-12  Score=117.53  Aligned_cols=81  Identities=22%  Similarity=0.288  Sum_probs=71.3

Q ss_pred             cccccCCCC--CccccCCC-CeEeecCCCCCHHHHHHHhhcC-C---------------ChhHHHHHHHhcCCCHHHHHH
Q psy938           11 TPIIESESG--EKFGKSAR-NAIWLDSKLSSSFELYQYLIRT-K---------------DSEVYDLLKLFSFDSLAAIED   71 (241)
Q Consensus        11 ~pLL~g~dG--~KmsKS~g-n~I~L~~~~Tsp~~~yq~~~~~-~---------------D~~v~~~l~~~t~l~~eei~~   71 (241)
                      +|+|+|++|  +|||||.+ |+|||++   +|+++++|++++ +               ++.+..|+++|++.+.+++++
T Consensus       179 ~~~i~~l~g~~~KMSKS~~~~~I~L~d---~~~~i~~KI~~a~td~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~  255 (280)
T cd00806         179 GAFLPGLQGPSKKMSKSDPNNAIFLTD---SPKEIKKKIMKAATDGGRTEHRRDGGGPGVSNLVEIYSAFFNDDDEELEE  255 (280)
T ss_pred             CCccccCCCCCCcccCCCCCCeEEeeC---CHHHHHHHHHhccCCCCCceecCCCCCCCcChHHHHHHHHhCCCHHHHHH
Confidence            599999998  49999998 9999999   999999999996 2               268899999999999999998


Q ss_pred             HHHHhh-cCCChHHHHHHHHHHHHh
Q psy938           72 FKRQNE-HKPEERRAQKKLAEDLTL   95 (241)
Q Consensus        72 i~~~~~-~~~~~~~~Kk~LA~~i~~   95 (241)
                      + +++. .+.+++++|+.||+.|++
T Consensus       256 ~-~~~~~g~~~~~~~K~~lae~i~~  279 (280)
T cd00806         256 I-DEYRSGGLGYGECKKLLAEAIQE  279 (280)
T ss_pred             H-HHhhcCCCCHHHHHHHHHHHHHh
Confidence            8 5554 458999999999999986

Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding

>PRK08560 tyrosyl-tRNA synthetase; Validated

Probab=99.36  E-value=2.2e-12  Score=119.13  Aligned_cols=93  Identities=19%  Similarity=0.288  Sum_probs=80.1

Q ss_pred             CCceeeecccccCCCCC--ccccCC-CCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcCCC--------
Q psy938            4 TGDGGLTTPIIESESGE--KFGKSA-RNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSFDS--------   65 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~--KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~l~--------   65 (241)
                      ..+++++.|+|||++|.  |||||. +|+|||++   +|+++++|++++       .++.+..|+++|.+..        
T Consensus       195 ~~p~~l~~~~l~~L~g~~~KMSKS~p~~~I~L~D---~~~~I~~KI~kA~t~~~~~~~n~v~~~~~~~~~~~~~~~~~~r  271 (329)
T PRK08560        195 KKPVCIHTPLLTGLDGGGIKMSKSKPGSAIFVHD---SPEEIRRKIKKAYCPPGEVEGNPVLEIAKYHIFPRYDPFVIER  271 (329)
T ss_pred             CCceEEEcCccCCCCCCCCCCcCCCCCCeecccC---CHHHHHHHHHhccCCCCCcCCCcHHHHHHHHhhccccceEEec
Confidence            46789999999999996  999999 99999999   999999999995       4578999999987531        


Q ss_pred             ---------HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           66 ---------LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        66 ---------~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                               .++++++++++..+ .++.++|+.||+.|++.+..
T Consensus       272 ~~~~g~~~~~~~~eel~~~y~~g~l~~~~lK~~la~~i~~~l~p  315 (329)
T PRK08560        272 PEKYGGDLEYESYEELERDYAEGKLHPMDLKNAVAEYLIEILEP  315 (329)
T ss_pred             hhhcCCCCCcCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence                     15688899998776 58999999999999888754

>PRK12284 tryptophanyl-tRNA synthetase; Reviewed

Probab=99.34  E-value=2e-12  Score=122.65  Aligned_cols=88  Identities=19%  Similarity=0.180  Sum_probs=73.4

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC-CC------------hhHHHHHHHhcCCCHHHHHHHH
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD------------SEVYDLLKLFSFDSLAAIEDFK   73 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D------------~~v~~~l~~~t~l~~eei~~i~   73 (241)
                      +....|+|+|+||+|||||.+|+|+|.+   ||+++++|++++ +|            +.+..|+++|+.  .+++++++
T Consensus       188 i~~~~~~I~gLdg~KMSKS~~n~I~L~D---s~~~I~kKI~~A~TDs~~~~~~~~pe~snLl~i~~~~~~--~~~~eel~  262 (431)
T PRK12284        188 IEESVATLPGLDGRKMSKSYDNTIPLFA---PREELKKAIFSIVTDSRAPGEPKDTEGSALFQLYQAFAT--PEETAAFR  262 (431)
T ss_pred             cccccccccCCCCccccCCCCCEeeecC---CHHHHHHHHhcCCCCCCCCCCCCCCCcchHHHHHHHhCC--cchHHHHH
Confidence            3345789999999999999999999999   999999999997 22            356666666653  46788888


Q ss_pred             HHhhcCCChHHHHHHHHHHHHhhccC
Q psy938           74 RQNEHKPEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        74 ~~~~~~~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      +++..+.++.++|+.||+.|++.+..
T Consensus       263 ~~~~~g~~~g~~K~~Lae~i~~~L~P  288 (431)
T PRK12284        263 QALADGIGWGDAKQRLFERIDRELAP  288 (431)
T ss_pred             HHHhcCCChHHHHHHHHHHHHHHHHH
Confidence            88876689999999999999988763

>PRK12285 tryptophanyl-tRNA synthetase; Reviewed

Probab=99.33  E-value=3.3e-12  Score=119.63  Aligned_cols=92  Identities=14%  Similarity=0.197  Sum_probs=77.9

Q ss_pred             CceeeecccccCCCCCccccCC-CCeEeecCCCCCHHHHHHHhhcC-CC-----------------hhHHHHHHHhcCCC
Q psy938            5 GDGGLTTPIIESESGEKFGKSA-RNAIWLDSKLSSSFELYQYLIRT-KD-----------------SEVYDLLKLFSFDS   65 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-~D-----------------~~v~~~l~~~t~l~   65 (241)
                      .+..+..|+|||++|+|||||. +|+|+|++   +|+++++|++++ +|                 +.+..|+++|...+
T Consensus       235 ~P~~l~~~~lpgL~G~KMSkS~~~s~I~L~D---~p~~I~kKI~kA~Td~~~t~~~~~~~~g~p~~~~v~~~l~~~~~~~  311 (368)
T PRK12285        235 KPSSTYHKFMPGLTGGKMSSSKPESAIYLTD---DPETVKKKIMKALTGGRATLEEQRKLGGEPDECVVYELLLYHLEED  311 (368)
T ss_pred             CchhHhhhcccCCCCCcCCCCCCCCeeeccC---CHHHHHHHHHhCcCCCCcccccccccCCCCCcchHHHHHHHHhcCC
Confidence            4455667899999999999998 67999999   999999999997 22                 56777777776555


Q ss_pred             HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           66 LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        66 ~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      .++++++.+.+..+ .++.++|+.||+.|++.+..
T Consensus       312 d~~~eei~~~y~~g~~~~g~~K~~lae~i~~~l~~  346 (368)
T PRK12285        312 DKELKEIYEECRSGELLCGECKKEAAEKIAEFLKE  346 (368)
T ss_pred             CccHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence            67899999999776 69999999999999999854

>PRK12556 tryptophanyl-tRNA synthetase; Provisional

Probab=99.30  E-value=4.1e-12  Score=117.50  Aligned_cols=87  Identities=20%  Similarity=0.215  Sum_probs=71.3

Q ss_pred             ecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCC-C---------hhHHHHHHHhcCC-CHHHHHHHHHHhhc
Q psy938           10 TTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTK-D---------SEVYDLLKLFSFD-SLAAIEDFKRQNEH   78 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~-D---------~~v~~~l~~~t~l-~~eei~~i~~~~~~   78 (241)
                      +.|+|+|+||+|||||.+|+|+|.+   +|+++++|++++. |         +++..++.++..+ +.++++++++++..
T Consensus       191 ~~~~l~gLdg~KMSKS~~n~I~L~D---~p~~I~kKI~ka~Td~~~~~~~~~p~~~~l~~i~~~~~~~~~~eei~~~y~~  267 (332)
T PRK12556        191 EGAILPGLDGRKMSKSYGNVIPLFA---EQEKLRKLIFKIKTDSSLPNEPKDPETSALFTIYKEFATEEEVQSMREKYET  267 (332)
T ss_pred             ccccccCCCCCCCCCCCCCcccccC---CHHHHHHHHHHhccCCCcccCCCCcchhHHHHHHHHHCCchhHHHHHHHHhc
Confidence            5899999999999999999999999   9999999999962 2         2344444444433 34678999998876


Q ss_pred             CCChHHHHHHHHHHHHhhccC
Q psy938           79 KPEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        79 ~~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      +.++.++|+.||+.|++.+..
T Consensus       268 ~~~~~~~K~~lae~i~~~l~p  288 (332)
T PRK12556        268 GIGWGDVKKELFRVVDRELAG  288 (332)
T ss_pred             CCChHHHHHHHHHHHHHHHHH
Confidence            778999999999999988764

>PRK00927 tryptophanyl-tRNA synthetase; Reviewed

Probab=99.29  E-value=7.3e-12  Score=115.82  Aligned_cols=84  Identities=20%  Similarity=0.192  Sum_probs=70.3

Q ss_pred             cccccCCCCC--ccccCCC---CeEeecCCCCCHHHHHHHhhcCC-Ch-----------------hHHHHHHHhcCCCHH
Q psy938           11 TPIIESESGE--KFGKSAR---NAIWLDSKLSSSFELYQYLIRTK-DS-----------------EVYDLLKLFSFDSLA   67 (241)
Q Consensus        11 ~pLL~g~dG~--KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~~-D~-----------------~v~~~l~~~t~l~~e   67 (241)
                      +|+|+|++|.  |||||.+   |+|+|++   +|+++++|++++. |+                 .+..|+++|+.   +
T Consensus       181 ~~~l~gL~g~~~KMSKS~~~~~~~I~l~D---~~~~I~~KI~~a~td~~~~~~~~~~~~~~p~~~~l~~~~~~~~~---~  254 (333)
T PRK00927        181 GARVMGLDGPTKKMSKSDPNDNNTINLLD---DPKTIAKKIKKAVTDSERLREIRYDLPNKPEVSNLLTIYSALSG---E  254 (333)
T ss_pred             cccccCCCCCCCCCCCCCCCCCCeEEeeC---CHHHHHHHHHhCCCCCCcccccccCCCCCCccccHHHHHHHhCC---C
Confidence            4999999995  9999998   8999999   9999999999984 43                 57778888875   4


Q ss_pred             HHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938           68 AIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGE  100 (241)
Q Consensus        68 ei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~  100 (241)
                      +++++.+++..+ .+++++|+.||+.|++.+..-
T Consensus       255 ~~eel~~~~~~g~~~~~~lK~~la~~i~~~l~pi  288 (333)
T PRK00927        255 SIEELEAEYEAGGKGYGDFKKDLAEAVVEFLAPI  288 (333)
T ss_pred             CHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHH
Confidence            566777777655 689999999999999987653

>PRK12282 tryptophanyl-tRNA synthetase II; Reviewed

Probab=99.28  E-value=1.2e-11  Score=114.54  Aligned_cols=87  Identities=21%  Similarity=0.294  Sum_probs=73.9

Q ss_pred             cccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcC-CC--------------hhHHHHHHHhcCCCHHHHHHHHH
Q psy938           11 TPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD--------------SEVYDLLKLFSFDSLAAIEDFKR   74 (241)
Q Consensus        11 ~pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D--------------~~v~~~l~~~t~l~~eei~~i~~   74 (241)
                      +|+|+|++| .|||||.+|+|||++   +|+++++|++++ +|              +.+..|+++|. .+.++++++++
T Consensus       185 ~~~i~~L~g~~KMSKS~~~~I~L~D---~pe~I~kKI~~A~td~~~~~~~~~~~~~~~~l~~~~~~f~-~~~~~~e~l~~  260 (333)
T PRK12282        185 AGRLPGLDGKAKMSKSLGNAIYLSD---DADTIKKKVMSMYTDPNHIRVEDPGKVEGNVVFTYLDAFD-PDKAEVAELKA  260 (333)
T ss_pred             CCcccCCCCCCcCCCCCCCeeeeeC---CHHHHHHHHHhCcCCCCCccCCCCCCCCcChHHHHHHHhC-CCCchHHHHHH
Confidence            789999999 799999999999999   999999999997 33              56777888763 13578899999


Q ss_pred             HhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938           75 QNEHK-PEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        75 ~~~~~-~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      ++..+ .++.++|+.||+.|++.+-.-.
T Consensus       261 ~y~~g~~~~~dlK~~lae~i~~~l~pir  288 (333)
T PRK12282        261 HYQRGGLGDVKCKRYLEEVLQELLAPIR  288 (333)
T ss_pred             HHhcCCCCcHHHHHHHHHHHHHHHHHHH
Confidence            98766 6999999999999999876543

>PRK12283 tryptophanyl-tRNA synthetase; Reviewed

Probab=99.27  E-value=6.1e-12  Score=118.41  Aligned_cols=84  Identities=14%  Similarity=0.134  Sum_probs=68.8

Q ss_pred             cccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC-CC--------------hhHHHHHHHhcCCCHHHHHHHHHH
Q psy938           11 TPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT-KD--------------SEVYDLLKLFSFDSLAAIEDFKRQ   75 (241)
Q Consensus        11 ~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-~D--------------~~v~~~l~~~t~l~~eei~~i~~~   75 (241)
                      .++|+|+||+|||||.+|+|+|.+   ||+++++|++++ +|              +.+.+++.+|+  +.++++++.+.
T Consensus       254 ~~~I~gLdg~KMSKS~~n~I~L~D---s~~~I~kKI~~a~TDs~~~~~~~~g~Pe~~nl~~i~~~~~--~~~~~~~i~~~  328 (398)
T PRK12283        254 ASKMPGLDGQKMSKSYGNTIGLRE---DPESVTKKIRTMPTDPARVRRTDPGDPEKCPVWQLHQVYS--DEETKEWVQKG  328 (398)
T ss_pred             CCcccCCCCCcCCCCCCCeeeCcC---CHHHHHHHHHhCCCCCcccccCCCCCCCcCHHHHHHHHhC--CChHHHHHHHH
Confidence            579999999999999999999999   999999999996 33              34555555554  34468888888


Q ss_pred             hhcC-CChHHHHHHHHHHHHhhccC
Q psy938           76 NEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        76 ~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      |+.+ .++.++|+.||+.|++.+..
T Consensus       329 ~~~g~~~~g~~K~~lae~v~e~L~~  353 (398)
T PRK12283        329 CRSAGIGCLECKQPVIDAILREQQP  353 (398)
T ss_pred             HhcCCCChHHHHHHHHHHHHHHHHH
Confidence            8765 68999999999999887653

>TIGR00233 trpS tryptophanyl-tRNA synthetase

Probab=99.23  E-value=3.2e-11  Score=111.41  Aligned_cols=88  Identities=19%  Similarity=0.217  Sum_probs=74.8

Q ss_pred             ecccccCCCCCccccCCCC-eEeecCCCCCHHHHHHHhhcC-CC---------------hhHHHHHHHhcCCC--HHHHH
Q psy938           10 TTPIIESESGEKFGKSARN-AIWLDSKLSSSFELYQYLIRT-KD---------------SEVYDLLKLFSFDS--LAAIE   70 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-~D---------------~~v~~~l~~~t~l~--~eei~   70 (241)
                      .+|.|+|++|+|||||.+| +|+|++   +|+++++|++++ .|               +++..++.+|++++  .++++
T Consensus       181 ~~~~l~gl~~~KMSKS~~~s~I~L~D---~~e~I~~KI~~a~td~~~~~~~~~~~~~g~~~l~~i~~~~~~~~~~~~~~~  257 (328)
T TIGR00233       181 FFPRLMGLSGKKMSKSDPNSAIFLTD---TPKQIKKKIRKAATDGGRVTLFEHREKGGVPNLLVIYQYLSFFLIDDDKLK  257 (328)
T ss_pred             ccCCCCCCCCCcCCCCCCCCeEeecC---CHHHHHHHHHhcCCCCCCCcccCcCCCCCCchHHHHHHHhhccCCCcchHH
Confidence            5789999999999999986 999999   999999999995 33               35778888888774  35788


Q ss_pred             HHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938           71 DFKRQNEHK-PEERRAQKKLAEDLTLLVHGE  100 (241)
Q Consensus        71 ~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~  100 (241)
                      ++.+.+..+ .++.++|+.||+.|.+.+..-
T Consensus       258 ~~~~~~~~g~~~~~~lK~~lae~i~~~l~pi  288 (328)
T TIGR00233       258 EIYEKYKSGKLLYGELKKALIEVLQEFLKEI  288 (328)
T ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHHHHHH
Confidence            888888766 689999999999999988763

This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this model.

>COG0180 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=99.13  E-value=1.4e-10  Score=106.30  Aligned_cols=83  Identities=18%  Similarity=0.242  Sum_probs=69.5

Q ss_pred             ccccCCCC-CccccCCCC-eEeecCCCCCHHHHHHHhhcC-CC---------------hhHHHHHHHhcCCCHHHHHHHH
Q psy938           12 PIIESESG-EKFGKSARN-AIWLDSKLSSSFELYQYLIRT-KD---------------SEVYDLLKLFSFDSLAAIEDFK   73 (241)
Q Consensus        12 pLL~g~dG-~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-~D---------------~~v~~~l~~~t~l~~eei~~i~   73 (241)
                      ++++|++| .|||||.+| +|+|.+   +|.++.+|++++ +|               +.+..|+.+|+.  .+++.++.
T Consensus       188 ~~i~gL~g~~KMSkS~~ns~I~L~D---~~~~i~kKI~~~~td~~~~~~~~~~g~Pe~~~l~~~~~~~~~--~~~~~ei~  262 (314)
T COG0180         188 ARLPGLDGPGKMSKSDPNSAIFLLD---DPKTIRKKIKKAATDGPTLIEYRKGGKPEVCNLFEIYSAFFE--DDSILEIE  262 (314)
T ss_pred             CcccCCCCCCcccccCCCCeeeccC---CHHHHHHHHHHhccCCCCccccCCCCCCCcchHHHHHHHhcC--CCcHHHHH
Confidence            79999999 899999999 999999   999999999993 33               355556555553  55666999


Q ss_pred             HHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           74 RQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        74 ~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      ++|+.| .++.+||+.||+.|.+.+-.
T Consensus       263 ~~~~~G~~~~ge~K~~lae~i~~fL~~  289 (314)
T COG0180         263 AEYRGGELGCGECKKELAEAIQEFLKP  289 (314)
T ss_pred             HHHhccccchHHHHHHHHHHHHHHHHH
Confidence            999887 79999999999999888765

>PTZ00348 tyrosyl-tRNA synthetase; Provisional

Probab=99.06  E-value=3.9e-10  Score=112.65  Aligned_cols=92  Identities=15%  Similarity=0.225  Sum_probs=77.1

Q ss_pred             CceeeecccccCCCC--CccccCC-CCeEeecCCCCCHHHHHHHhhcC----------------------CChhHHHHHH
Q psy938            5 GDGGLTTPIIESESG--EKFGKSA-RNAIWLDSKLSSSFELYQYLIRT----------------------KDSEVYDLLK   59 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG--~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~----------------------~D~~v~~~l~   59 (241)
                      +++.+..|+|+|++|  .|||||. +|+|+|++   +|+++++|++++                      +++.+..|++
T Consensus       204 kpvil~~~~LpGL~gg~~KMSKS~p~naI~L~D---spe~I~kKI~kA~td~~~~~~~~~~d~g~p~~~~e~npvl~i~~  280 (682)
T PTZ00348        204 KPVILSHHMLAGLKQGQAKMSKSDPDSAIFMED---TEEDVARKIRQAYCPRVKQSASEITDDGAPVATDDRNPVLDYFQ  280 (682)
T ss_pred             CceecccccCcCCCCCCCcCCCCCCCCeecccC---CHHHHHHHHHhCCCCCCcCcccccCCCCCccccCCCCcHHHHHH
Confidence            456667899999974  6999999 68999999   999999999998                      2267888999


Q ss_pred             HhcCCCH-----------HHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           60 LFSFDSL-----------AAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        60 ~~t~l~~-----------eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      ++.|...           ++++++++.+..+ .++.++|+.||+.|++.+..
T Consensus       281 ~~if~~~g~~~~i~~~~~~~~eele~~y~~g~l~~~dlK~~lae~l~~~L~P  332 (682)
T PTZ00348        281 CVVYARPGAVATIDGTTYATYEDLEQAFVSDEVSEEALKSCLIDEVNALLEP  332 (682)
T ss_pred             HHhccccchhcccCCcccCcHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence            8865322           5688999999765 69999999999999998865

>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=98.82  E-value=8.9e-09  Score=68.78  Aligned_cols=44  Identities=23%  Similarity=0.251  Sum_probs=41.0

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +|..+|..+|+++|+++|+++|.+|+|+|||+++++|++.+...
T Consensus         2 RLd~~L~~~~~~~sr~~a~~~I~~g~V~VNg~~v~~~~~~v~~~   45 (48)
T PF01479_consen    2 RLDKFLSRLGLASSRSEARRLIKQGRVKVNGKVVKDPSYIVKPG   45 (48)
T ss_dssp             BHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEESSTTSBESTT
T ss_pred             CHHHHHHHcCCcCCHHHHHHhcCCCEEEECCEEEcCCCCCCCCc
Confidence            57889999999999999999999999999999999999988765

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....

>PLN02886 aminoacyl-tRNA ligase

Probab=98.78  E-value=9.5e-09  Score=96.87  Aligned_cols=85  Identities=19%  Similarity=0.128  Sum_probs=65.4

Q ss_pred             cccccCCCC--CccccCCC---CeEeecCCCCCHHHHHHHhhcCC-C------------hhHHHHHHHhcCCCHHHHHHH
Q psy938           11 TPIIESESG--EKFGKSAR---NAIWLDSKLSSSFELYQYLIRTK-D------------SEVYDLLKLFSFDSLAAIEDF   72 (241)
Q Consensus        11 ~pLL~g~dG--~KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~~-D------------~~v~~~l~~~t~l~~eei~~i   72 (241)
                      .++|++++|  .|||||..   |+|+|.|   +|+++++|++++. |            +.+.+++.+|..++..+++++
T Consensus       239 ~~ri~~L~~g~~KMSKS~p~~~s~I~L~D---s~e~I~kKI~~a~TD~~~~i~~~~p~~p~v~nl~~i~~~~~~~~~eei  315 (389)
T PLN02886        239 GARVMSLTDGTSKMSKSAPSDQSRINLLD---PPDVIANKIKRCKTDSFPGLEFDNPERPECNNLLSIYQLVTGKTKEEV  315 (389)
T ss_pred             cceeeeCCCCCCcCCCCCCCCCCeEEecC---CHHHHHHHHhcCCCCCCCCccCCCCCCcccccHHHHHHHccCCCHHHH
Confidence            347888854  69999984   6999999   9999999999972 2            344556666655545566777


Q ss_pred             HHHhhcCCChHHHHHHHHHHHHhhccC
Q psy938           73 KRQNEHKPEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        73 ~~~~~~~~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      .+++. +.++.++|+.||+.|++.+..
T Consensus       316 ~~~~~-~~~~g~~K~~Lae~I~~~L~P  341 (389)
T PLN02886        316 LAECG-DMRWGDFKPLLTDALIEHLSP  341 (389)
T ss_pred             HHHhc-CCCCchHHHHHHHHHHHHHHH
Confidence            77765 568889999999999888754

>KOG2144|consensus

Probab=98.18  E-value=5.4e-06  Score=75.21  Aligned_cols=93  Identities=18%  Similarity=0.230  Sum_probs=76.5

Q ss_pred             CceeeecccccCCC-CCccccCCCC-eEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcCCCHH--------
Q psy938            5 GDGGLTTPIIESES-GEKFGKSARN-AIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSFDSLA--------   67 (241)
Q Consensus         5 ~~~~lt~pLL~g~d-G~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~l~~e--------   67 (241)
                      ....+..|.|||+. |+|||+|..+ .|.|-+   +|.+++.++.+.       .++....|+++..|.-.+        
T Consensus       205 KrihLmnpMvPGL~q~~KMSsSd~~SkIdllD---~~~~V~kKI~kAfCePg~ve~Ng~L~fvkyvvfP~~~e~~~~~i~  281 (360)
T KOG2144|consen  205 KRIHLMNPMVPGLAQGEKMSSSDPLSKIDLLD---EPADVNKKIKKAFCEPGNVEGNGCLSFVKYVVFPIFEEFGVEVID  281 (360)
T ss_pred             cceeecCCCCccccccCccccCCccccccccc---CHHHHHHHHHHhcCCCCCcCCCcHHHHHHHHHhhhHHhcCceeec
Confidence            45667889999998 7999999977 599999   999999999985       678888888876653222        


Q ss_pred             ------------HHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCH
Q psy938           68 ------------AIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGE  100 (241)
Q Consensus        68 ------------ei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~  100 (241)
                                  ..+++++.+..+ .||.++|+-|+..|.+++.+-
T Consensus       282 r~ek~GG~~tf~syed~e~~y~~~~lhPgDLK~~l~~alN~lL~~i  327 (360)
T KOG2144|consen  282 RPEKFGGNKTFKSYEDIEKDYEEGELHPGDLKKGLEKALNELLQPI  327 (360)
T ss_pred             chhhcCCcchhHHHHHHHHHHHhCCcChHHHHHHHHHHHHHHHHHH
Confidence                        177888888766 799999999999999998753

>PF13275 S4_2: S4 domain; PDB: 1P9K_A

Probab=97.99  E-value=2.9e-06  Score=60.91  Aligned_cols=47  Identities=21%  Similarity=0.157  Sum_probs=32.6

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+.|.++|..+|+++|.+||+.+|++|.|+|||+..+.....+...
T Consensus         6 e~I~L~qlLK~~glv~sGGeAK~~I~~g~V~VNGe~e~rrg~Kl~~G   52 (65)
T PF13275_consen    6 EYITLGQLLKLAGLVSSGGEAKALIQEGEVKVNGEVETRRGKKLRPG   52 (65)
T ss_dssp             S---HHHHHHHHTS-SSSSTTSHHHHHHHHEETTB----SS----SS
T ss_pred             CcEEHHHHHhHcCCcccHHHHHHHHHcCceEECCEEccccCCcCCCC
Confidence            35789999999999999999999999999999999998877666544

>PRK11507 ribosome-associated protein; Provisional

Probab=97.91  E-value=6.5e-05  Score=54.64  Aligned_cols=47  Identities=15%  Similarity=0.157  Sum_probs=40.8

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +-+.|.++|+.+|+++|.++|+-+|++|.|+|||+..+.-...+-..
T Consensus        10 e~I~L~QlLK~~~~v~SGG~AK~~I~eg~V~VNGeve~rRgkKl~~G   56 (70)
T PRK11507         10 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAG   56 (70)
T ss_pred             CeEEHHHHHhhhCcccChHHHHHHHHcCceEECCEEecccCCCCCCC
Confidence            34789999999999999999999999999999999887766555544

>KOG2713|consensus

Probab=97.90  E-value=1.7e-05  Score=71.96  Aligned_cols=80  Identities=19%  Similarity=0.196  Sum_probs=62.6

Q ss_pred             CC-CccccCCCC---eEeecCCCCCHHHHHHHhhcC-CC------------hhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938           18 SG-EKFGKSARN---AIWLDSKLSSSFELYQYLIRT-KD------------SEVYDLLKLFSFDSLAAIEDFKRQNEHKP   80 (241)
Q Consensus        18 dG-~KmsKS~gn---~I~L~~~~Tsp~~~yq~~~~~-~D------------~~v~~~l~~~t~l~~eei~~i~~~~~~~~   80 (241)
                      |+ +|||||.+|   +|.|.|   ||..+-+|+.+. +|            +.|.+++.++..++-..++++++++ .+.
T Consensus       207 dpekKMSKSd~n~~s~I~l~D---S~~~I~~Ki~ka~TD~~~~vtYd~~~RpgvsNLlni~aaVt~~s~eeV~~~~-a~~  282 (347)
T KOG2713|consen  207 DPEKKMSKSDPNPKSRINLTD---SPDLIVKKIKKAQTDNTSGVTYDPANRPGVSNLLNIYAAVTGKSIEEVVEES-ANM  282 (347)
T ss_pred             ChhhhcccCCCCCcceEEecC---CHHHHHHHHHHHhcccccceeeCCccccchhHHHHHHHHHcCCCHHHHHHHh-ccC
Confidence            66 699999976   799999   999999999996 22            4677777777666555666666543 345


Q ss_pred             ChHHHHHHHHHHHHhhccCHH
Q psy938           81 EERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        81 ~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      ..++.|-.+|+.|++.+.+-.
T Consensus       283 ~~~~fK~~vaeAvie~L~PIr  303 (347)
T KOG2713|consen  283 STADFKDNVAEAVIEHLAPIR  303 (347)
T ss_pred             CHHHHHHHHHHHHHHHhccHH
Confidence            678999999999999888744

>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes

Probab=97.90  E-value=3e-05  Score=53.38  Aligned_cols=44  Identities=25%  Similarity=0.268  Sum_probs=38.1

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++.++|.+.+...|+++++++|++|+|+|||+++++++..+...
T Consensus         2 rl~~~l~~~~~~~sr~~~~~~i~~g~V~vn~~~~~~~~~~v~~~   45 (70)
T cd00165           2 RLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPG   45 (70)
T ss_pred             cHHHHHHHhccccCHHHHHHHHHcCCEEECCEEccCCccCcCCC
Confidence            56788888877789999999999999999999998888766544

>PRK04051 rps4p 30S ribosomal protein S4P; Validated

Probab=97.86  E-value=4.9e-05  Score=64.72  Aligned_cols=94  Identities=16%  Similarity=0.143  Sum_probs=60.7

Q ss_pred             HHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCHHHHHHH
Q psy938           89 LAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLT  168 (241)
Q Consensus        89 LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~SksEARRl  168 (241)
                      +|..+.. ...+.........-+.||.-+.-+  .  ...|..+. .+.+..+   -..+|..+|+..|++.|..+||++
T Consensus        54 ~Ar~Ll~-~~~~~r~~~~~~Ll~kL~~~Gil~--~--~~~L~~vl-~L~v~~~---lerRLd~il~r~gla~S~~~Ar~l  124 (177)
T PRK04051         54 QARSLLA-LPPEERAKEEEQLLGKLKRYGILK--E--NATLDDVL-SLTVEDI---LERRLQTIVYRKGLARTPKQARQF  124 (177)
T ss_pred             HHHHHhc-CCchHHHHHHHHHHHHHHHcCCCC--C--CCCHHHHH-hccHHHH---HHhHHHHHHHHccCcCCHHHHHHH
Confidence            4444443 223444445556667777765311  1  11233222 1211111   124788899999999999999999


Q ss_pred             HHhCCeEEccEEecCCCCccCCC
Q psy938          169 ISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       169 I~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      |.+|-|+|||++|++|.+.+..+
T Consensus       125 I~hGhV~V~g~~V~~Ps~~V~~~  147 (177)
T PRK04051        125 IVHGHIAVNGRRVTSPSYLVSVE  147 (177)
T ss_pred             HHcCCEEECCEEeCCCCeECCCC
Confidence            99999999999999999988754

>smart00363 S4 S4 RNA-binding domain

Probab=97.77  E-value=6.9e-05  Score=50.03  Aligned_cols=44  Identities=25%  Similarity=0.314  Sum_probs=37.4

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++..+|...+...|+++++++|.+|+|+|||+++++++..+...
T Consensus         2 rl~~~l~~~~~~~s~~~~~~~i~~g~i~vng~~~~~~~~~l~~g   45 (60)
T smart00363        2 RLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPG   45 (60)
T ss_pred             cHHHHHHHcCcccCHHHHHHHHHcCCEEECCEEecCCCeEeCCC
Confidence            45667888877789999999999999999999998888777654

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA

Probab=97.76  E-value=5.5e-05  Score=52.72  Aligned_cols=46  Identities=15%  Similarity=0.096  Sum_probs=40.6

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+|.++|...++..|++.++++|++|.|+|||.+++.|+..+...
T Consensus         8 ~~rLd~~L~~~~~~~SR~~~k~li~~G~V~VNg~~~~~~~~~l~~G   53 (59)
T TIGR02988         8 YITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPG   53 (59)
T ss_pred             HHHHHHHHHHcCCccCHHHHHHHHHcCCEEECCEEccCCCCCCCCC
Confidence            5778889998888889999999999999999999998888777655

This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.

>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional

Probab=97.60  E-value=0.00037  Score=56.78  Aligned_cols=60  Identities=13%  Similarity=0.165  Sum_probs=49.6

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEE
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIA  212 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i  212 (241)
                      .++|..+|+.+++++|++.|.++|.+|.|.|||++ +.|...+..+      ..+.|+.|...+.+.
T Consensus         8 ~~RlDk~L~~~rl~ktRs~A~~lI~~G~V~vnG~~-~Kps~~V~~g------d~l~v~~~~~~~~v~   67 (133)
T PRK10348          8 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQR-SKPSKIVELN------ATLTLRQGNDERTVI   67 (133)
T ss_pred             cccHHHHHHHcCccccHHHHHHHHHCCCEEECCEE-CCCCCccCCC------CEEEEEECCEEEEEE
Confidence            46899999999999999999999999999999999 7888766544      356788887665433

>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type)

Probab=97.58  E-value=0.00019  Score=60.28  Aligned_cols=95  Identities=15%  Similarity=0.163  Sum_probs=62.4

Q ss_pred             HHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCHHHHHHH
Q psy938           89 LAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLT  168 (241)
Q Consensus        89 LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~SksEARRl  168 (241)
                      +|.++..+- ++.-.......-+.||.-+.-  .+ +...+..+. .+.+..+.   ..+|.-++...|+++|-.+||.+
T Consensus        54 ~Ar~L~~l~-d~~r~~~~~~LL~kL~~~Gll--~e-~~~~Ld~vl-~Ltv~~~l---eRRL~~vv~r~g~a~s~~~Arql  125 (162)
T TIGR01018        54 AARELLGLD-DEQRLFEGNQLLRRLVRLGIL--DE-ENAKLDDVL-GLTVEDFL---ERRLQTQVFKKGLARTIHQARQL  125 (162)
T ss_pred             HHHHHHcCC-cHHHHHHHHHHHHHHHHcCCC--cc-ccCCHHHHH-hccHHHHH---HHhHhhHhhhccCcCCHHHHHHH
Confidence            566665555 555555556677778775531  10 011233222 11111110   23577778899999999999999


Q ss_pred             HHhCCeEEccEEecCCCCccCCC
Q psy938          169 ISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       169 I~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      |.+|-|+|||++|++|.+.+..+
T Consensus       126 I~hgHI~V~~~~V~~Ps~~V~~~  148 (162)
T TIGR01018       126 IVHGHIAVDGRRVTSPSYIVRRE  148 (162)
T ss_pred             hhCCCeeECCEEeccCceEecCC
Confidence            99999999999999999888765

This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.

>PTZ00348 tyrosyl-tRNA synthetase; Provisional

Probab=97.33  E-value=0.00072  Score=68.27  Aligned_cols=83  Identities=10%  Similarity=0.161  Sum_probs=64.7

Q ss_pred             eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC------CChhHHHHHHHhcCCC----------------
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT------KDSEVYDLLKLFSFDS----------------   65 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~------~D~~v~~~l~~~t~l~----------------   65 (241)
                      |+..|++.++   +|||  +++|++++   |+.++.+|++++      .++.|..|++|+ +..                
T Consensus       549 ~l~~~~~~~~---~~s~--~s~i~~~D---~~~~i~~Ki~kA~Cpp~~~~Npvl~~~~y~-~~~~~~~~i~R~e~~Gg~~  619 (682)
T PTZ00348        549 ALHRPGAAPA---VLGA--DDVLYLDD---NDMDIRRKIKKAYSAPNEEANPVISVAQHL-LAQQGALSIERGEANGGNV  619 (682)
T ss_pred             cccccccccC---CCCC--CCeeeecC---CHHHHHHHHHhCCCCCCCCCCcHHHHHHHH-hcCCCeEEEecccccCCCe
Confidence            4444444333   4544  88999999   999999999997      568899999987 321                


Q ss_pred             -HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           66 -LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        66 -~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                       -+.++++++.+.++ .||.++|..+|+.+.+++..
T Consensus       620 ~y~s~eeL~~dy~~g~lhP~DLK~av~~~l~~~l~p  655 (682)
T PTZ00348        620 AYNTPEALVADCGSGALHPADLKAAVSQLLLDRSAA  655 (682)
T ss_pred             eeCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence             11389999999877 79999999999999998765

>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]

Probab=97.32  E-value=0.00056  Score=61.22  Aligned_cols=46  Identities=24%  Similarity=0.195  Sum_probs=40.9

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSA  192 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~  192 (241)
                      .++|.++|..+|++ |++||.++|.+|.|+|||+.++++...+..+.
T Consensus         2 ~~RL~K~La~~G~~-SRr~ae~lI~~G~V~VnG~v~~~~~~~v~~~~   47 (248)
T COG1187           2 SMRLNKFLAEAGVG-SRREAEKLIEEGRVTVNGKVATLGGVVVDPDD   47 (248)
T ss_pred             ccchHHHHHHcCCC-CHHHHHHHHHcCCEEECCEEeccCCeEeCCCC
Confidence            35788999999998 99999999999999999999999887777653

>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis]

Probab=97.26  E-value=0.00037  Score=61.92  Aligned_cols=45  Identities=24%  Similarity=0.324  Sum_probs=41.4

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++|..+|++-|++.|++.|+++|..|-|+|||++++.|.+.+..+
T Consensus         3 ~RLD~~Lv~rgl~~sR~~A~~~I~~G~V~Vng~~v~KP~~~V~~~   47 (245)
T COG1189           3 MRLDALLVERGLFESREKAKELILAGNVLVNGEKVTKPSQLVDID   47 (245)
T ss_pred             chHHHHHHHccchhhHHHHHHHHHcCeEEECCEEecCcceecCCC
Confidence            578899999999999999999999999999999999999887643

>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]

Probab=97.10  E-value=0.0018  Score=47.48  Aligned_cols=45  Identities=18%  Similarity=0.082  Sum_probs=39.0

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLS  189 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~  189 (241)
                      +-+.|.++|..+|+++|.++|+-+|++|.|+|||+.-+.-...+-
T Consensus        10 e~I~L~qlLK~~g~i~sGG~AK~~i~eg~V~vNGe~EtRRgkKlr   54 (73)
T COG2501          10 EFITLGQLLKLAGLIESGGQAKAFIAEGEVKVNGEVETRRGKKLR   54 (73)
T ss_pred             ceEEHHHHHHHhCcccCcHHHHHHHHCCeEEECCeeeeccCCEee
Confidence            357899999999999999999999999999999998776554443

>TIGR01017 rpsD_bact ribosomal protein S4, bacterial/organelle type

Probab=97.05  E-value=0.0011  Score=57.47  Aligned_cols=45  Identities=24%  Similarity=0.243  Sum_probs=40.7

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..+|..+|++.|+++|+++|.+|.|.|||.+++.|.+.+..+
T Consensus        90 ~RLD~~L~~~g~~~SR~~ArqlI~~G~V~VNgk~v~~ps~~V~~G  134 (200)
T TIGR01017        90 SRLDNVVYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPG  134 (200)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCCEEECCEEeCCCCCCCCCC
Confidence            567788889999999999999999999999999999998877654

This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.

>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis]

Probab=97.02  E-value=0.00079  Score=58.66  Aligned_cols=45  Identities=22%  Similarity=0.274  Sum_probs=40.5

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..+....|+++|..+||.||..|-|.|||.+|+.|.+.+..+
T Consensus        94 rRLd~vVyR~GfA~T~~qARQlV~HGHI~VnGk~V~iPSy~V~~g  138 (205)
T COG0522          94 RRLDNVVYRLGFAKTRRQARQLVSHGHILVNGKRVNIPSYLVSPG  138 (205)
T ss_pred             HHHHHHHHHhcccccHHHHHHHhhcceEEECCEEeccCcEEecCC
Confidence            356667778999999999999999999999999999999988765

>KOG2145|consensus

Probab=96.99  E-value=0.0024  Score=58.46  Aligned_cols=95  Identities=16%  Similarity=0.209  Sum_probs=68.8

Q ss_pred             CceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhcC----------------CChhH---HHHHHHhc
Q psy938            5 GDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIRT----------------KDSEV---YDLLKLFS   62 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~----------------~D~~v---~~~l~~~t   62 (241)
                      .+.-+..-.+|.+.|  .|||-|..| +|+|++   +|.++..++.+-                .+++|   ..||++|-
T Consensus       260 Kpali~stffpaLqG~~~KMSASdpns~Ifltd---t~~qIk~KI~~~afSGGr~tiEeHRe~GGn~dVDV~~~YLsFFl  336 (397)
T KOG2145|consen  260 KPALIHSTFFPALQGAQTKMSASDPNSAIFLTD---TAKQIKNKINKYAFSGGRDTIEEHRELGGNPDVDVSFQYLSFFL  336 (397)
T ss_pred             CcceeehhhchhhhCcccccccCCCCceEEecC---cHHHHHHHHHHhhccCCcchHHHHHHhCCCCcceehHHHHHHHh
Confidence            344566677888999  599999977 699999   999999999874                23344   44555443


Q ss_pred             CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           63 FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        63 ~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      . +.++.+++...+..| .--.+.|+.+-+.++..|.--.++
T Consensus       337 d-DD~kLeq~r~~Y~~G~mltgEmKk~~ievLq~~V~~hQa~  377 (397)
T KOG2145|consen  337 D-DDDKLEQIRKDYTSGEMLTGEMKKLCIEVLQEFVSRHQAA  377 (397)
T ss_pred             c-cHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence            1 566788888777666 455788999999888887644433

>TIGR00478 tly hemolysin TlyA family protein

Probab=96.95  E-value=0.0014  Score=57.89  Aligned_cols=44  Identities=25%  Similarity=0.246  Sum_probs=39.1

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +|..+|+..|++.|+++|+++|.+|.|+|||+++++|...+..+
T Consensus         1 RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~v~k~s~~V~~~   44 (228)
T TIGR00478         1 RLDILLVRRGLFESREKAKRLILKGFVLVNGKKVDKPSALVDFD   44 (228)
T ss_pred             CHHHHHHHcCCccHHHHHHHHHHCCcEEECCEEeCCCCCCCCCC
Confidence            36678899999999999999999999999999999998877644

Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. At least two members of this protein family have been characterized indirectly as pore-forming hemolysins, one from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. However, homology domains in this protein suggest methyltransferase activity (pfam01728) and RNA-binding activity (pfam01479).

>CHL00113 rps4 ribosomal protein S4; Reviewed

Probab=96.94  E-value=0.0015  Score=56.81  Aligned_cols=45  Identities=20%  Similarity=0.212  Sum_probs=40.8

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..+|...|+++|+++||++|.+|.|.|||.+++.|.+.+..+
T Consensus        89 ~RLD~~L~r~g~~~SR~~ArqlI~~G~V~VNGk~v~~ps~~Vk~G  133 (201)
T CHL00113         89 MRLDNILFRLGMAPTIPAARQLVNHGHILVNGRIVDIPSYRCKPK  133 (201)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHCCcEEECCEEecCccccCCCC
Confidence            468889999999999999999999999999999999998877654

>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]

Probab=96.89  E-value=0.0036  Score=48.55  Aligned_cols=60  Identities=17%  Similarity=0.189  Sum_probs=49.7

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEE
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIA  212 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i  212 (241)
                      .++|...|..+.++++++-|+.+|.+|.|.|||.++ .|...+..+      ..+-|+.|.+.+-+-
T Consensus         8 ~mRLDKwL~~aR~~KrRslAk~~~~~GrV~vNG~~a-KpS~~VK~G------D~l~i~~~~~~~~v~   67 (100)
T COG1188           8 RMRLDKWLWAARFIKRRSLAKEMIEGGRVKVNGQRA-KPSKEVKVG------DILTIRFGNKEFTVK   67 (100)
T ss_pred             ceehHHHHHHHHHhhhHHHHHHHHHCCeEEECCEEc-ccccccCCC------CEEEEEeCCcEEEEE
Confidence            478999999999999999999999999999999988 566555544      467899998876443

>PTZ00155 40S ribosomal protein S9; Provisional

Probab=96.78  E-value=0.0012  Score=56.55  Aligned_cols=45  Identities=11%  Similarity=0.017  Sum_probs=40.8

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|.-++...|+++|..+||.+|.+|-|.|||++|++|.+.+..+
T Consensus       107 RRL~~iv~r~g~A~ti~~ARqlI~HGHI~V~~~~V~~Ps~~V~~~  151 (181)
T PTZ00155        107 RRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSFLVRVD  151 (181)
T ss_pred             HhhhhHHHhccCcCCHHHhhhheeCCCEEECCEEeccCceEeccC
Confidence            356777889999999999999999999999999999999988765

>PRK05327 rpsD 30S ribosomal protein S4; Validated

Probab=96.68  E-value=0.0032  Score=54.72  Aligned_cols=45  Identities=24%  Similarity=0.297  Sum_probs=39.9

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..+|...|++.|+++|+++|..|.|.|||.+++.|.+.+..+
T Consensus        93 ~RLD~iL~~~g~~~SR~~arqlI~~G~V~VNgk~v~~ps~~v~~G  137 (203)
T PRK05327         93 SRLDNVVYRLGFAPTRRQARQLVSHGHILVNGKKVNIPSYRVKPG  137 (203)
T ss_pred             HHHHHHHHHcCccCCHHHHHHHHHCCcEEECCEEECCCCcCCCCC
Confidence            457778888999999999999999999999999998898877655

>PLN00189 40S ribosomal protein S9; Provisional

Probab=96.37  E-value=0.0016  Score=56.28  Aligned_cols=44  Identities=14%  Similarity=0.104  Sum_probs=39.2

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +|.-++...|+++|..+||.+|.+|-|.|||++|++|.+.+..+
T Consensus       110 RL~~vv~r~g~a~si~~ARqlI~hgHI~V~~~~V~~Ps~~V~~~  153 (194)
T PLN00189        110 RLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSFMVRVD  153 (194)
T ss_pred             hhceeeeecCCcCCHHHHHHheeCCCEeECCEEEecCcEEEecC
Confidence            45556678999999999999999999999999999999988755

>TIGR03069 PS_II_S4 photosystem II S4 domain protein

Probab=96.16  E-value=0.012  Score=52.87  Aligned_cols=45  Identities=16%  Similarity=0.146  Sum_probs=37.4

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+|. .+...++.-|++.|+++|++|.|.|||..+++|++.+...
T Consensus       183 s~RLD-~lls~~~~~SRs~a~~lI~~G~V~VNg~~v~~~s~~v~~g  227 (257)
T TIGR03069       183 SLRID-AIASAGFGLSRSKIVDQIKAGRLRLNWKTVTQPSRELKVG  227 (257)
T ss_pred             cccHH-HHHHhhhhhhHHHHHHHHHCCeEEECCEEcCCCCCcCCCC
Confidence            45666 5556677669999999999999999999999998877654

Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium.

>PRK10700 23S rRNA pseudouridylate synthase B; Provisional

Probab=95.97  E-value=0.012  Score=53.77  Aligned_cols=42  Identities=12%  Similarity=0.030  Sum_probs=35.9

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP  190 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~  190 (241)
                      ++|.++|..+|.+ |+++|+++|++|.|+|||..+ ++...+..
T Consensus         3 ~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNG~~~-~~g~~V~~   44 (289)
T PRK10700          3 EKLQKVLARAGHG-SRREIESIIEAGRVSVDGKIA-TLGDRVEV   44 (289)
T ss_pred             hhHHHHHHHCCCC-CHHHHHHHHHcCCEEECCEec-cCCCEeCC
Confidence            5688899999976 999999999999999999977 57766653

>cd00818 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases

Probab=95.95  E-value=0.0026  Score=58.96  Aligned_cols=28  Identities=21%  Similarity=0.212  Sum_probs=23.6

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecC
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      -.++...+...+|+|||||.||+||+++
T Consensus       285 ~~~~hg~~~~~~g~KmSKS~gn~i~~~~  312 (338)
T cd00818         285 NVIVHGFVLDEDGRKMSKSLGNYVDPQE  312 (338)
T ss_pred             eEEEEeeEECCCCCCCCCCCCCcCCHHH
Confidence            4456678888899999999999998874

Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>PRK10475 23S rRNA pseudouridine synthase F; Provisional

Probab=95.86  E-value=0.012  Score=53.67  Aligned_cols=44  Identities=14%  Similarity=0.223  Sum_probs=37.0

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +++|.++|..+|++ |+++|+++|.+|.|.|||+++ .++..+...
T Consensus         6 ~~RL~k~La~~g~~-SRr~a~~lI~~G~V~VNGk~v-~~~~~V~~g   49 (290)
T PRK10475          6 STRLNKYISESGIC-SRREADRYIEQGNVFINGKRA-TIGDQVKAG   49 (290)
T ss_pred             HHHHHHHHHhCCCC-CHHHHHHHHHCCcEEECCEEc-cCCCCcCCC
Confidence            56789999999976 999999999999999999987 466666543

>PRK00750 lysK lysyl-tRNA synthetase; Reviewed

Probab=95.31  E-value=0.012  Score=57.83  Aligned_cols=32  Identities=22%  Similarity=0.233  Sum_probs=27.0

Q ss_pred             CCCCceeeecccccCCCCCccccCCCCeEeec
Q psy938            2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      +..+++.+..+++...+|+|||||.||.|.++
T Consensus       261 g~~~P~~~~y~~v~~~~G~KMSKSkGN~i~~~  292 (510)
T PRK00750        261 GGEPPEPFVYELFLDKKGEKISKSKGNVITIE  292 (510)
T ss_pred             CCCCCeeeeeeeEEeCCCCcccccCCCccCHH
Confidence            34567788889999888999999999999765

>PLN00051 RNA-binding S4 domain-containing protein; Provisional

Probab=95.21  E-value=0.06  Score=48.73  Aligned_cols=45  Identities=18%  Similarity=0.175  Sum_probs=36.7

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+|..++. +++--|++.|..+|++|.|+||+..+++|++.+..+
T Consensus       191 s~RLD~vla-~~~~~SRsk~~~lI~~g~V~vN~~~v~~~s~~v~~g  235 (267)
T PLN00051        191 SLRLDALAS-AGFRMSRSKLVDLISSGDVRVNWREVTKNGTTLKTG  235 (267)
T ss_pred             cccHHHHHH-HHhccCHHHHHHHHHcCcEEECCEEcCCCCCCCCCC
Confidence            355666544 455679999999999999999999999999887765

>cd00668 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases

Probab=94.87  E-value=0.0096  Score=54.28  Aligned_cols=44  Identities=18%  Similarity=0.123  Sum_probs=29.4

Q ss_pred             eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFS   62 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t   62 (241)
                      .++...+...+|+|||||.||+||+++       +-+.    -++++.+|+-+.+
T Consensus       260 ~~~~g~~~~~~g~KmSKS~gn~v~~~d-------~~~~----~~~da~R~~l~~~  303 (312)
T cd00668         260 LLVHGFVLDEGGQKMSKSKGNVIDPSD-------VVEK----YGADALRYYLTSL  303 (312)
T ss_pred             eEECcEEEcCCCccccccCCCcCCHHH-------HHHH----cCcHHHHHHHHhc
Confidence            445566777777999999999998875       2222    2356666655443

Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function.

>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]

Probab=94.80  E-value=0.067  Score=47.93  Aligned_cols=64  Identities=16%  Similarity=0.207  Sum_probs=49.3

Q ss_pred             HHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCccc----CCCeEEEEec---cccEEEEEE
Q psy938          150 LELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHIL----PNSLTLLRVE---VSANIIAKS  214 (241)
Q Consensus       150 ~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~----~~~~~llr~G---Kk~~~~i~~  214 (241)
                      +|.+...++--|++.|..+|.+|-|+||.+.++++++.+..+ |++    .|+.-+++.+   ||.-++|++
T Consensus       183 LD~vis~~~~~SR~~a~~lIe~g~VkVN~k~v~~~s~~v~~G-DliSirG~GR~~i~~i~g~TKKdK~ri~l  253 (257)
T COG2302         183 LDVVISEGFGLSRAKAQQLIEKGKVKVNWKVVDKASYEVQEG-DLISIRGFGRLKILEINGVTKKDKFRITL  253 (257)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHcCceEEeeEEeccccceeccC-CEEEEeccccEEEEeecCccccccEEEEE
Confidence            456667777779999999999999999999999999988876 443    4666666666   555555554

>PRK12418 cysteinyl-tRNA synthetase; Provisional

Probab=94.71  E-value=0.012  Score=55.93  Aligned_cols=25  Identities=24%  Similarity=0.324  Sum_probs=19.8

Q ss_pred             eecccccCCCCCccccCCCCeEeec
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      ....-..+.+|+|||||.||.|++.
T Consensus       249 w~H~g~l~~~G~KMSKSlGN~i~~~  273 (384)
T PRK12418        249 YVHAGMIGLDGEKMSKSRGNLVFVS  273 (384)
T ss_pred             EEECCEECCCCCcccCcCCCcCCHH
Confidence            3444566789999999999998665

>COG0060 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=94.69  E-value=0.016  Score=60.35  Aligned_cols=23  Identities=35%  Similarity=0.424  Sum_probs=20.5

Q ss_pred             eeecccccCCCCCccccCCCCeE
Q psy938            8 GLTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      ++|.-.+.+.+|+|||||.||+|
T Consensus       589 vltHGfvlDe~GrKMSKSlGN~v  611 (933)
T COG0060         589 VLTHGFVLDEKGRKMSKSLGNVV  611 (933)
T ss_pred             HhhcccEECCCCCCccccCCCcC
Confidence            56777888999999999999997

>cd00812 LeuRS_core catalytic core domain of leucyl-tRNA synthetases

Probab=94.63  E-value=0.0089  Score=54.82  Aligned_cols=19  Identities=37%  Similarity=0.366  Sum_probs=17.0

Q ss_pred             CCCCCccccCCCCeEeecC
Q psy938           16 SESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~   34 (241)
                      ..+|+|||||.||+||+++
T Consensus       270 ~~~g~KmSkS~Gn~v~~~d  288 (314)
T cd00812         270 LLEGEKMSKSKGNVVTPDE  288 (314)
T ss_pred             ecCccccCCcCCCCCCHHH
Confidence            4689999999999999886

Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases

Probab=94.55  E-value=0.012  Score=55.54  Aligned_cols=42  Identities=17%  Similarity=0.111  Sum_probs=29.6

Q ss_pred             eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHH
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKL   60 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~   60 (241)
                      .+....+.+.+|+|||||.||+|++++       +-+.    -+.+..+|+-+
T Consensus       330 v~~hg~v~~~~g~KMSKS~Gn~v~~~d-------ll~~----~g~Da~R~~ll  371 (382)
T cd00817         330 VYLHGLVRDEDGRKMSKSLGNVIDPLD-------VIDG----YGADALRFTLA  371 (382)
T ss_pred             eEeeeeEECCCCCCccccCCCCCCHHH-------HHHh----cCcHHHHHHHH
Confidence            455667888999999999999997664       3332    23566666544

Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.

>PF00133 tRNA-synt_1: tRNA synthetases class I (I, L, M and V); InterPro: IPR002300 The aminoacyl-tRNA synthetases (6

Probab=94.50  E-value=0.022  Score=56.87  Aligned_cols=24  Identities=33%  Similarity=0.347  Sum_probs=16.7

Q ss_pred             eeecccccCCCCCccccCCCCeEe
Q psy938            8 GLTTPIIESESGEKFGKSARNAIW   31 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~   31 (241)
                      .++...+.+.+|+|||||.||+|.
T Consensus       548 v~~hG~vld~~G~KMSKS~GNvi~  571 (601)
T PF00133_consen  548 VITHGFVLDEDGRKMSKSKGNVID  571 (601)
T ss_dssp             EEEE--EEETTSSB-BTTTTB--B
T ss_pred             eeecccccccceeecccCCCcccC
Confidence            467788999999999999999983

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1OBC_A 2AJH_B 4ARI_A 2AJG_B 4AQ7_D 2AJI_B 4ARC_A 4AS1_A 1QU3_A 1QU2_A ....

>PRK11893 methionyl-tRNA synthetase; Reviewed

Probab=94.36  E-value=0.017  Score=55.85  Aligned_cols=42  Identities=21%  Similarity=0.147  Sum_probs=27.1

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ..++.-.+. .+|+|||||.||+||+.+  +.-+++.++=++++.
T Consensus       286 ~~~~~g~v~-~~G~KMSKS~GN~i~~~dll~~~g~DalR~~ll~~  329 (511)
T PRK11893        286 RVFAHGFLT-LDGEKMSKSLGNVIDPFDLVDEYGVDAVRYFLLRE  329 (511)
T ss_pred             EEEeeccEE-ECCeeecccCCcEEcHHHHHHHcCcHHHHHHHHhc
Confidence            344455555 489999999999999863  123455555445443

>PTZ00427 isoleucine-tRNA ligase, putative; Provisional

Probab=94.23  E-value=0.031  Score=60.08  Aligned_cols=24  Identities=17%  Similarity=0.183  Sum_probs=21.1

Q ss_pred             eeecccccCCCCCccccCCCCeEe
Q psy938            8 GLTTPIIESESGEKFGKSARNAIW   31 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~   31 (241)
                      .++..++.+.+|+|||||.||+|.
T Consensus       707 VlvHG~Vld~dG~KMSKSlGNvID  730 (1205)
T PTZ00427        707 LICNGLVLASDGKKMSKRLKNYPD  730 (1205)
T ss_pred             eEEccEEEcCCCCCcccCCCCCCC
Confidence            567788999999999999999873

>PLN02381 valyl-tRNA synthetase

Probab=94.22  E-value=0.026  Score=59.97  Aligned_cols=23  Identities=35%  Similarity=0.482  Sum_probs=21.1

Q ss_pred             eeecccccCCCCCccccCCCCeE
Q psy938            8 GLTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      .++.+++.+.+|+|||||.||.|
T Consensus       642 v~~hG~V~D~~G~KMSKS~GNvI  664 (1066)
T PLN02381        642 VYLHPMIRDAHGRKMSKSLGNVI  664 (1066)
T ss_pred             heecceEECCCCCCCCCCCCCCC
Confidence            46788999999999999999998

>PLN02882 aminoacyl-tRNA ligase

Probab=94.14  E-value=0.034  Score=59.55  Aligned_cols=26  Identities=23%  Similarity=0.219  Sum_probs=22.1

Q ss_pred             eeeecccccCCCCCccccCCCCeEee
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWL   32 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L   32 (241)
                      -.++..++.+.+|+|||||.||+|+-
T Consensus       600 ~VivhG~vlde~G~KMSKSlGNvIdP  625 (1159)
T PLN02882        600 NLICNGLVLAEDGKKMSKSLKNYPDP  625 (1159)
T ss_pred             eeEEccEEECCCCCCcccCCCCCCCH
Confidence            35677888999999999999999854

>PRK05743 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=94.13  E-value=0.033  Score=58.25  Aligned_cols=25  Identities=32%  Similarity=0.207  Sum_probs=21.1

Q ss_pred             eeecccccCCCCCccccCCCCeEee
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWL   32 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L   32 (241)
                      .++...+.+.+|+|||||.||.|..
T Consensus       579 vl~HG~vld~~G~KMSKSlGNvIdP  603 (912)
T PRK05743        579 VLTHGFTVDGKGRKMSKSLGNVIDP  603 (912)
T ss_pred             eEEeeeEECCCCCCCCCCCCCcCCH
Confidence            4567788899999999999998843

>PRK05729 valS valyl-tRNA synthetase; Reviewed

Probab=94.07  E-value=0.02  Score=59.47  Aligned_cols=43  Identities=21%  Similarity=0.084  Sum_probs=29.5

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      -.+...++.+.+|+|||||.||.|+..+  ++-.++.++=++++.
T Consensus       506 ~v~~hG~v~d~~G~KMSKSlGNvIdP~dvi~~yGaDalR~~ll~~  550 (874)
T PRK05729        506 DVYIHGLVRDEQGRKMSKSKGNVIDPLDLIDKYGADALRFTLAAL  550 (874)
T ss_pred             heEEeeeEECCCCCCcccCCCCCCCHHHHHHHhChHHHHHHHHhC
Confidence            3556778899999999999999997652  112344455445543

>PRK14900 valS valyl-tRNA synthetase; Provisional

Probab=93.97  E-value=0.021  Score=60.64  Aligned_cols=41  Identities=22%  Similarity=0.165  Sum_probs=29.4

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++..++.+.+|+|||||.||.|+..+  ++-.++.++=+++.
T Consensus       525 V~~hG~v~d~~G~KMSKSkGNvIdP~dvIe~yGaDalR~~L~~  567 (1052)
T PRK14900        525 VYLHPMVRDEKGQKMSKTKGNVIDPLVITEQYGADALRFTLAA  567 (1052)
T ss_pred             eEecccEECCCCCCccCCCCCCCCHHHHHHHhCcHHHHHHHHh
Confidence            567788999999999999999998763  12234445444544

>PRK13208 valS valyl-tRNA synthetase; Reviewed

Probab=93.89  E-value=0.02  Score=58.86  Aligned_cols=41  Identities=12%  Similarity=0.135  Sum_probs=28.2

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++...+.+.+|+|||||.||+|+..+  +.-.++.++=+++.
T Consensus       520 v~~hg~v~~~~G~KMSKS~GN~i~p~~~i~~yg~D~lR~~l~~  562 (800)
T PRK13208        520 IMISGMVLDPDGKKMSKSKGNVVTPEELLEKYGADAVRYWAAS  562 (800)
T ss_pred             EEEeeEEECCCCCCCCCCCCCCCCHHHHHHHcCccHHHHHHhc
Confidence            356677888999999999999998652  11234455545553

>TIGR03447 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase

Probab=93.89  E-value=0.018  Score=55.16  Aligned_cols=21  Identities=29%  Similarity=0.376  Sum_probs=17.4

Q ss_pred             cccCCCCCccccCCCCeEeec
Q psy938           13 IIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus        13 LL~g~dG~KmsKS~gn~I~L~   33 (241)
                      =....+|+|||||.||.|.+.
T Consensus       280 g~l~~~G~KMSKSlGN~i~~~  300 (411)
T TIGR03447       280 GMIGLDGEKMSKSLGNLVFVS  300 (411)
T ss_pred             CEECcCCCCccCcCCCCCCHH
Confidence            355779999999999998665

Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione.

>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=93.83  E-value=0.037  Score=57.34  Aligned_cols=22  Identities=32%  Similarity=0.489  Sum_probs=19.7

Q ss_pred             eecccccCCCCCccccCCCCeE
Q psy938            9 LTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      +-..|+-+.+|+|||||.||.|
T Consensus       513 ~ihGLVrDe~G~KMSKS~GNvI  534 (877)
T COG0525         513 YIHGLVRDEQGRKMSKSKGNVI  534 (877)
T ss_pred             EEeeeEEcCCCCCCcccCCCcC
Confidence            4568999999999999999987

>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=93.79  E-value=0.025  Score=54.73  Aligned_cols=35  Identities=29%  Similarity=0.255  Sum_probs=26.2

Q ss_pred             cCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938           15 ESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus        15 ~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ...+|+|||||.||.|-+-+  +.-+|..++=++++.
T Consensus       262 l~i~geKMSKSLGNfiti~d~l~~~~p~~lR~~lls~  298 (464)
T COG0215         262 LNIDGEKMSKSLGNFITVRDLLKKYDPEVLRLFLLSS  298 (464)
T ss_pred             eeecCcCcccccCCeeEHHHHHhhcCHHHHHHHHHHH
Confidence            45689999999999998764  224677777666664

>PRK06039 ileS isoleucyl-tRNA synthetase; Reviewed

Probab=93.74  E-value=0.024  Score=59.73  Aligned_cols=42  Identities=24%  Similarity=0.161  Sum_probs=29.1

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      .+...++.+.+|+|||||.||+|+..+  ++-.++.++=++++.
T Consensus       579 v~~hG~Vld~~G~KMSKSlGNvIdP~dli~~yGaDalR~~lls~  622 (975)
T PRK06039        579 VLVHGHVLDEDGQKMSKSLGNYVDPFEVFDKYGADALRWYLLSS  622 (975)
T ss_pred             EEEeeeEECCCCCCcCCCCCCcCCHHHHHHHhChHHHHHHHHhC
Confidence            455667788899999999999997652  122455555555554

>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional

Probab=93.73  E-value=0.12  Score=47.74  Aligned_cols=45  Identities=16%  Similarity=0.009  Sum_probs=37.5

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP  190 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~  190 (241)
                      +.+|.++|.......|++.++++|.+|.|+|||.++..++..+..
T Consensus        17 g~RLd~~L~~~~~~~Sr~~~~~lI~~G~V~VNg~~v~~~~~~v~~   61 (325)
T PRK11180         17 GQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLG   61 (325)
T ss_pred             CccHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCcCcCC
Confidence            678999998765456999999999999999999998777655543

>PRK13804 ileS isoleucyl-tRNA synthetase; Provisional

Probab=93.66  E-value=0.045  Score=57.59  Aligned_cols=27  Identities=33%  Similarity=0.310  Sum_probs=22.3

Q ss_pred             eeeecccccCCCCCccccCCCCeEeec
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      -.++...+.+.+|+|||||.||.|...
T Consensus       616 ~V~~HG~vld~~G~KMSKSlGNvIdP~  642 (961)
T PRK13804        616 AVLTHGFTLDEKGEKMSKSLGNTVSPQ  642 (961)
T ss_pred             hEEEeccEECCCCCCccCCCCCcCCHH
Confidence            356778889999999999999998543

>PTZ00419 valyl-tRNA synthetase-like protein; Provisional

Probab=93.65  E-value=0.034  Score=58.65  Aligned_cols=23  Identities=30%  Similarity=0.459  Sum_probs=20.9

Q ss_pred             eeecccccCCCCCccccCCCCeE
Q psy938            8 GLTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      .++.+++.+.+|+|||||.||.|
T Consensus       572 v~~HG~v~d~~G~KMSKSlGNvI  594 (995)
T PTZ00419        572 VFLHAMVRDSQGEKMSKSKGNVI  594 (995)
T ss_pred             HhccceEECCCCCCcccCCCCcC
Confidence            56778899999999999999998

>PF01406 tRNA-synt_1e: tRNA synthetases class I (C) catalytic domain; InterPro: IPR015803 The aminoacyl-tRNA synthetases (6

Probab=93.62  E-value=0.035  Score=51.04  Aligned_cols=19  Identities=37%  Similarity=0.407  Sum_probs=11.5

Q ss_pred             CCCCCccccCCCCeEeecC
Q psy938           16 SESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~   34 (241)
                      ..+|+|||||.||.|.+.+
T Consensus       247 ~~~g~KMSKSlgN~~~i~d  265 (300)
T PF01406_consen  247 NVDGEKMSKSLGNFITIRD  265 (300)
T ss_dssp             EETTCE--TTTT---BHHH
T ss_pred             hhcCccccccCCCEEEHHH
Confidence            3489999999999998874

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Cysteinyl-tRNA synthetase (6.1.1.16 from EC) is an alpha monomer and belongs to class Ia.; GO: 0000166 nucleotide binding, 0004817 cysteine-tRNA ligase activity, 0005524 ATP binding, 0006423 cysteinyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3SP1_B 3TQO_A 3C8Z_B 1LI5_B 1LI7_B 1U0B_B.

>PRK04313 30S ribosomal protein S4e; Validated

Probab=93.47  E-value=0.25  Score=44.06  Aligned_cols=73  Identities=14%  Similarity=0.081  Sum_probs=51.5

Q ss_pred             CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      .++|.=+|.. .|++.+.+||++.+.||-|.|||...+|+.+-+-.= |+     .+..|-+|-=-|.+|.+.+...+-|
T Consensus        37 siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlm-DVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea  115 (237)
T PRK04313         37 SIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRVRKDYKFPVGLM-DVISIPETGEYYRVLPDEKGRLVLIPISEEEA  115 (237)
T ss_pred             ccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEEEcccccCcCce-eEEEEccCCCeEEEEECCCCcEEEEECChHHc
Confidence            5677777775 799999999999999999999999999988755322 11     1223445555556666666554444

>TIGR00422 valS valyl-tRNA synthetase

Probab=93.35  E-value=0.029  Score=58.22  Aligned_cols=43  Identities=21%  Similarity=0.079  Sum_probs=30.0

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      -.+...++.+.+|+|||||.||+|+..+  +.-.++.++=++++.
T Consensus       511 ~v~~hG~v~d~~G~KMSKS~GN~i~p~~~i~~ygaDalR~~l~~~  555 (861)
T TIGR00422       511 EVYIHGLVRDEQGRKMSKSLGNVIDPLDVIEKYGADALRFTLASL  555 (861)
T ss_pred             eEEEeeEEECCCCCCCCcCCCCCCCHHHHHHHhChHHHHHHHHhC
Confidence            3456788899999999999999998653  112445555555544

The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase.

>TIGR00392 ileS isoleucyl-tRNA synthetase

Probab=93.32  E-value=0.03  Score=58.09  Aligned_cols=41  Identities=22%  Similarity=0.148  Sum_probs=26.5

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ++...+.+.+|+|||||.||+|+..+  ++-.++.++=++++.
T Consensus       599 ~~hG~vl~~~G~KMSKSkGNvI~p~d~i~~yGaDalR~~ll~~  641 (861)
T TIGR00392       599 ITHGFTLDEKGRKMSKSLGNVVDPLKVINKYGADILRLYVASS  641 (861)
T ss_pred             EecceEECCCCCCcCCCCCCCCCHHHHHHHcCHHHHHHHHHhC
Confidence            34556667899999999999997652  122344444444443

The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms.

>PLN02943 aminoacyl-tRNA ligase

Probab=93.29  E-value=0.031  Score=58.81  Aligned_cols=41  Identities=22%  Similarity=0.058  Sum_probs=29.2

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .+....+.+.+|+|||||.||.|+..+  ++-.|+.++=++..
T Consensus       570 v~~hg~v~~~~G~KMSKS~GN~i~p~~~i~~ygaDalR~~l~~  612 (958)
T PLN02943        570 VYLHGLIRDSQGRKMSKTLGNVIDPLDTIKEFGTDALRFTLAL  612 (958)
T ss_pred             EEEeccEECCCCCcccCcCCCCCCHHHHHHhcCChHHHHHHHh
Confidence            456788889999999999999998763  12245555544443

>cd00672 CysRS_core catalytic core domain of cysteinyl tRNA synthetase

Probab=93.23  E-value=0.023  Score=49.56  Aligned_cols=25  Identities=28%  Similarity=0.147  Sum_probs=19.9

Q ss_pred             ecccccCCCCCccccCCCCeEeecC
Q psy938           10 TTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      ...-+.+.+|+|||||.||.|.+.+
T Consensus       163 ~h~~~v~~~g~KMSKs~Gn~v~~~d  187 (213)
T cd00672         163 LHTGHLTIDGEKMSKSLGNFITVRD  187 (213)
T ss_pred             EEEEEEeccCcchhhcCCCccCHHH
Confidence            3444567899999999999997765

Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

>PRK12300 leuS leucyl-tRNA synthetase; Reviewed

Probab=92.98  E-value=0.034  Score=58.06  Aligned_cols=40  Identities=23%  Similarity=0.221  Sum_probs=27.6

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ++...+.. +|+|||||.||+|+..+  ++-.++.++=++++.
T Consensus       566 ~~hG~vl~-~G~KMSKS~GNvVdp~eii~~yGaDalRl~L~~~  607 (897)
T PRK12300        566 VVNGFVLL-EGKKMSKSKGNVIPLRKAIEEYGADVVRLYLTSS  607 (897)
T ss_pred             EEcceEEE-CCccccCcCCCCCCHHHHHHHcChHHHHHHHHhC
Confidence            44555666 89999999999998762  223556666666654

>PRK12268 methionyl-tRNA synthetase; Reviewed

Probab=92.85  E-value=0.029  Score=55.18  Aligned_cols=32  Identities=34%  Similarity=0.431  Sum_probs=21.3

Q ss_pred             CCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .+|+|||||.||+||..+  ++-.++.++=+++.
T Consensus       330 ~~G~KMSKS~GN~I~p~dli~~yGaDalR~~ll~  363 (556)
T PRK12268        330 LEGGKFSKSRGWGIWVDDALERYPPDYLRYYLAA  363 (556)
T ss_pred             ECCeeeccCCCcccCHHHHHHHcCcHHHHHHHHh
Confidence            489999999999998773  11234444444443

>PRK00133 metG methionyl-tRNA synthetase; Reviewed

Probab=92.84  E-value=0.039  Score=55.78  Aligned_cols=38  Identities=24%  Similarity=0.329  Sum_probs=25.3

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhh
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLI   47 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~   47 (241)
                      +....++. +|+|||||.||+||..+  ++-.++.++=+++
T Consensus       318 ~~hg~v~~-~G~KMSKS~GNvV~p~dlie~ygaDalR~~ll  357 (673)
T PRK00133        318 FAHGFLTV-EGAKMSKSRGTFIWARTYLDHLDPDYLRYYLA  357 (673)
T ss_pred             eeeccEEe-cCCcccccCCcccCHHHHHHHcCchHHHHHHH
Confidence            34455555 99999999999999763  1234455555555

>PLN02843 isoleucyl-tRNA synthetase

Probab=92.84  E-value=0.053  Score=57.16  Aligned_cols=27  Identities=30%  Similarity=0.218  Sum_probs=22.8

Q ss_pred             eeeecccccCCCCCccccCCCCeEeec
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      -.++.+.+.+.+|+|||||.||.|...
T Consensus       597 ~v~~HG~vld~~G~KMSKSlGNvI~p~  623 (974)
T PLN02843        597 SVLTHGFVLDEKGFKMSKSLGNVVDPR  623 (974)
T ss_pred             eEEEeccEECCCCCCcCCCCCCcCCHH
Confidence            356778899999999999999998654

>TIGR00005 rluA_subfam pseudouridine synthase, RluA family

Probab=92.81  E-value=0.19  Score=45.40  Aligned_cols=46  Identities=17%  Similarity=0.097  Sum_probs=36.5

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+|.++|......-|+++++++|.+|.|+|||.++.+++..+...
T Consensus         5 g~rLd~~L~~~~~~~Sr~~~~kli~~G~V~VNg~~~~~~~~~v~~g   50 (299)
T TIGR00005         5 GQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGKVTANPKLKVKDG   50 (299)
T ss_pred             chhHHHHHHHhcccCCHHHHHHHHHCCcEEECCEeccCcccCCCCC
Confidence            5778899987654239999999999999999997666666666543

modifies uracil-65 in transfer RNAs to pseudouridine.

>cd00814 MetRS_core catalytic core domain of methioninyl-tRNA synthetases

Probab=92.79  E-value=0.03  Score=51.38  Aligned_cols=35  Identities=23%  Similarity=0.247  Sum_probs=24.1

Q ss_pred             CCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHh
Q psy938           16 SESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLF   61 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~   61 (241)
                      ..+|+|||||.||+||+.+       +-    ..-.+++.+|+-+.
T Consensus       275 ~~~g~kmSkS~gn~i~~~~-------~l----~~~~~d~~R~~l~~  309 (319)
T cd00814         275 TVEGKKMSKSRGNVVDPDD-------LL----ERYGADALRYYLLR  309 (319)
T ss_pred             EECCeeecccCCcccCHHH-------HH----HHcCchHHHHHHHh
Confidence            4589999999999998874       21    22355666766543

Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function.

>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6

Probab=92.67  E-value=0.025  Score=53.67  Aligned_cols=18  Identities=50%  Similarity=0.776  Sum_probs=16.3

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      .+|+|||||.||+||.++
T Consensus       323 ~~g~K~SkS~gn~i~~~~  340 (391)
T PF09334_consen  323 LDGEKMSKSRGNVIWPDD  340 (391)
T ss_dssp             ETTCCEETTTTESSBHHH
T ss_pred             ECCeeccccCCcccCHHH
Confidence            589999999999999874

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....

>PRK10839 16S rRNA pseudouridylate synthase A; Provisional

Probab=92.66  E-value=0.26  Score=43.10  Aligned_cols=43  Identities=14%  Similarity=-0.018  Sum_probs=33.8

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++.++|...+ .-|++.++++|++|.|+|||.++.+++..+...
T Consensus         2 rld~~L~~~~-~~Sr~~~~~li~~g~V~VNg~~~~~~~~~l~~g   44 (232)
T PRK10839          2 RLDKFISQQL-GVSRAIAGRELRANRVTVDGEIVKNGAFKLLPE   44 (232)
T ss_pred             cHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeccCCcCcCCC
Confidence            4566777665 358999999999999999999887666666543

>KOG0432|consensus

Probab=92.52  E-value=0.05  Score=56.12  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.8

Q ss_pred             eeecccccCCCCCccccCCCCeE
Q psy938            8 GLTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      .+..|++-+..|+|||||.||.|
T Consensus       580 V~LH~mVRDa~GRKMSKSLGNVI  602 (995)
T KOG0432|consen  580 VLLHGLVRDAHGRKMSKSLGNVI  602 (995)
T ss_pred             eeechhhccccccccchhhcccc
Confidence            45679999999999999999987

>PTZ00223 40S ribosomal protein S4; Provisional

Probab=92.32  E-value=0.46  Score=43.17  Aligned_cols=73  Identities=14%  Similarity=0.086  Sum_probs=52.6

Q ss_pred             CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      .++|.=+|.. .+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+     .+..|-+|-=-|.+|.+.++...-|
T Consensus        38 siPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~~PvGlM-DVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA  116 (273)
T PTZ00223         38 CLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKPRKDGKYPAGFM-DVVEIPKTGDRFRILYDVKGRFALVKVSEAEA  116 (273)
T ss_pred             ccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEEEccCCCCCcee-EEEEEcCCCCeEEEEECCCCcEEEEEcChHHc
Confidence            5677777875 799999999999999999999999999988765322 11     1233555655566666666655544

>PLN02610 probable methionyl-tRNA synthetase

Probab=92.27  E-value=0.067  Score=55.31  Aligned_cols=34  Identities=21%  Similarity=0.218  Sum_probs=25.1

Q ss_pred             CCCCCccccCCCCeEeecCCC---CCHHHHHHHhhcC
Q psy938           16 SESGEKFGKSARNAIWLDSKL---SSSFELYQYLIRT   49 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~~~---Tsp~~~yq~~~~~   49 (241)
                      ..+|+|||||.||.||..+-.   -+++.++=|+++.
T Consensus       343 ~~eG~KMSKS~GNvV~p~~~i~~~yg~D~lRyyLl~~  379 (801)
T PLN02610        343 NYEGGKFSKSKGVGVFGNDAKDTNIPVEVWRYYLLTN  379 (801)
T ss_pred             ecCCceecCcCCcccCHHHHHhccCCchHhHHHhhhc
Confidence            468999999999999988532   3566666666664

>TIGR00395 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family

Probab=92.26  E-value=0.049  Score=57.16  Aligned_cols=40  Identities=18%  Similarity=0.195  Sum_probs=27.7

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      +....+.. +|+|||||.||.|++.+  ++-+++.++=++++.
T Consensus       609 ~~~G~vl~-~G~KMSKSlGNvI~p~d~i~~yGaDalRl~Ll~~  650 (938)
T TIGR00395       609 VVNGYVML-EGKKMSKSKGNVLTLEQAVEKFGADVARLYIADA  650 (938)
T ss_pred             EEeceEEe-CCccccCcCCCCCCHHHHHHHcChHHHHHHHHhc
Confidence            34445554 89999999999998763  223566666666665

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS.

>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=92.26  E-value=0.08  Score=52.60  Aligned_cols=18  Identities=33%  Similarity=0.355  Sum_probs=15.8

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      .+|+|||||.||.||-++
T Consensus       329 ~~G~KmSKSrG~~V~~~~  346 (558)
T COG0143         329 LEGQKMSKSRGNVVDPDE  346 (558)
T ss_pred             ECCccccccCCcEEeHHH
Confidence            578999999999998773

>PRK00260 cysS cysteinyl-tRNA synthetase; Validated

Probab=92.26  E-value=0.042  Score=53.20  Aligned_cols=37  Identities=24%  Similarity=0.186  Sum_probs=24.5

Q ss_pred             ccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           12 PIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .-+.+.+|+|||||.||.|.+.+  +.-+|..++=++++
T Consensus       257 ~g~v~~~G~KMSKS~GN~i~~~dll~~~~~d~lR~~ll~  295 (463)
T PRK00260        257 NGFVTVNGEKMSKSLGNFFTIRDLLKKYDPEVLRFFLLS  295 (463)
T ss_pred             ccEEccCCCcccCcCCCCCCHHHHHHHcCchHhHHHHHh
Confidence            34456899999999999997753  12345555544444

>PLN02224 methionine-tRNA ligase

Probab=92.10  E-value=0.042  Score=55.16  Aligned_cols=33  Identities=21%  Similarity=0.249  Sum_probs=23.5

Q ss_pred             CCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           16 SESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      ..+|+|||||.||+||..+  +.-+|+.++=|+++
T Consensus       361 ~~eG~KMSKS~GN~i~p~e~l~~ygaD~~R~yLl~  395 (616)
T PLN02224        361 TKDGMKMGKSLGNTLEPFELVQKFGPDAVRYFFLR  395 (616)
T ss_pred             ecCCccccccCCccCCHHHHHHHcCcHHHHHHHHh
Confidence            5799999999999998873  22345555555554

>PRK14535 cysS cysteinyl-tRNA synthetase; Provisional

Probab=92.06  E-value=0.19  Score=51.05  Aligned_cols=41  Identities=24%  Similarity=0.217  Sum_probs=26.6

Q ss_pred             eeeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      |=+..-.|. .+|+|||||.||.|.+.+  ++-+|..++=++++
T Consensus       495 yWmHnG~V~-vdGeKMSKSLGN~it~~dlLe~ygpdalRl~lLs  537 (699)
T PRK14535        495 YWLHNGFIR-VDGEKMSKSLGNFFTIREVLKQYDPEVVRFFILR  537 (699)
T ss_pred             EEEECCeEe-eCCCccCCCCCCcCCHHHHHHhCCHHHHHHHHHc
Confidence            445555565 899999999999986542  12345555544444

>TIGR00435 cysS cysteinyl-tRNA synthetase

Probab=91.99  E-value=0.041  Score=53.35  Aligned_cols=18  Identities=28%  Similarity=0.174  Sum_probs=16.0

Q ss_pred             CCCCCccccCCCCeEeec
Q psy938           16 SESGEKFGKSARNAIWLD   33 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~   33 (241)
                      ..+|+|||||.||.|.+.
T Consensus       260 ~~~g~KMSKS~GN~i~~~  277 (465)
T TIGR00435       260 MIDNEKMSKSLGNFFTVR  277 (465)
T ss_pred             EecCccccccCCCcCCHH
Confidence            479999999999999775

This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln).

>PLN02946 cysteine-tRNA ligase

Probab=91.68  E-value=0.062  Score=53.39  Aligned_cols=26  Identities=19%  Similarity=0.183  Sum_probs=19.8

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      -+..-.|. .+|+|||||.||.|.+.+
T Consensus       311 W~H~G~v~-~~G~KMSKSlGN~itl~d  336 (557)
T PLN02946        311 WIHNGFVT-VDSEKMSKSLGNFFTIRQ  336 (557)
T ss_pred             eeEeeEEE-eCCCCcCCcCCCcCCHHH
Confidence            34444555 799999999999997763

>cd00418 GlxRS_core catalytic core domain of glutamyl-tRNA and glutaminyl-tRNA synthetase

Probab=91.57  E-value=0.16  Score=45.06  Aligned_cols=46  Identities=22%  Similarity=0.130  Sum_probs=31.4

Q ss_pred             CCceeeecccccCCCCCccccCCCCe-E-eecCCCCCHHHHHHHhhcC
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNA-I-WLDSKLSSSFELYQYLIRT   49 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~-I-~L~~~~Tsp~~~yq~~~~~   49 (241)
                      ..+....+|+|.+.+|+||||+.++. | ++-..--+|..+..++..+
T Consensus       136 ~~P~~~H~pll~~~~g~KLSKr~~~~~i~~~r~~G~~p~ai~~~l~~l  183 (230)
T cd00418         136 EPPRFYHFPRLLLEDGTKLSKRKLNTTLRALRRRGYLPEALRNYLALI  183 (230)
T ss_pred             CCCeEEEeeeeeCCCCCCccCcCCCcCHHHHHHCCCcHHHHHHHHHHc
Confidence            45667899999999999999999872 2 2212223566666665544

Glutamyl-tRNA synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Glu or Gln, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea, cellular organelles, and some bacteria lack GlnRS. In these cases, the "non-discriminating" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme. The discriminating form of GluRS differs from GlnRS and the non-discriminating form of GluRS in their C-terminal anti-codon bind

>PTZ00118 40S ribosomal protein S4; Provisional

Probab=91.37  E-value=0.68  Score=41.85  Aligned_cols=73  Identities=15%  Similarity=-0.019  Sum_probs=51.0

Q ss_pred             CCcHHHHHH-hcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSL-ATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv-~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      .++|.=+|. ..+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+     .+..|-+|-=-|.+|.+.++...-|
T Consensus        41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m-DVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA  119 (262)
T PTZ00118         41 CLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKVRTDCTYPVGFM-DVVSLTKTNEYFRLLYDTKGRFVPHKITNEEA  119 (262)
T ss_pred             ccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEEEccCCCCCcee-EEEEEcCCCCeEEEEECCCccEEEEEcCHHHh
Confidence            467777776 4689999999999999999999999999987655321 11     1223445555556666666654444

>TIGR00398 metG methionyl-tRNA synthetase

Probab=91.21  E-value=0.072  Score=52.10  Aligned_cols=38  Identities=24%  Similarity=0.226  Sum_probs=23.4

Q ss_pred             ecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           10 TTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      +.-.+..- |+|||||.||+||+++  +.-.++.++=++++
T Consensus       317 ~~g~v~~~-g~KmSKS~Gn~i~~~d~i~~~g~D~lR~~l~~  356 (530)
T TIGR00398       317 SHGYLTVE-GGKMSKSLGNVVDPSDLLARFGADILRYYLLK  356 (530)
T ss_pred             eeccEEEC-CceecccCCceecHHHHHHHcCchHHHHHHhh
Confidence            34444433 9999999999998773  11234444444444

The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma

>PRK12267 methionyl-tRNA synthetase; Reviewed

Probab=91.15  E-value=0.059  Score=54.19  Aligned_cols=32  Identities=25%  Similarity=0.200  Sum_probs=22.3

Q ss_pred             CCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .+|+|||||.||+||..+  +.-+|+.++=|+++
T Consensus       295 ~eg~KMSKS~GN~i~p~d~l~~ygaD~lR~~L~~  328 (648)
T PRK12267        295 MKDGKMSKSKGNVVDPEELVDRYGLDALRYYLLR  328 (648)
T ss_pred             ECCceecccCCcccCHHHHHHHcCCcHHHHHHHh
Confidence            368999999999999763  12345555555654

>PLN00036 40S ribosomal protein S4; Provisional

Probab=91.13  E-value=0.76  Score=41.54  Aligned_cols=73  Identities=11%  Similarity=-0.016  Sum_probs=51.5

Q ss_pred             CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      .++|.=+|.. .+++.+.+||++.+.||-|.|||...+|+.+-+-.= |+     .+..|-+|-=-|.+|.+.++...-|
T Consensus        41 slPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkvr~D~~fPvG~m-DVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA  119 (261)
T PLN00036         41 CLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKVRTDKTYPAGFM-DVISIPKTNENFRLLYDTKGRFRLHRINDEEA  119 (261)
T ss_pred             ccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEEeccCCCCCcee-EEEEEcCCCCeEEEEECCCceEEEEEcChHHc
Confidence            4677777764 699999999999999999999999999988765321 11     1223445555566666666654444

>KOG0437|consensus

Probab=90.96  E-value=0.41  Score=49.12  Aligned_cols=77  Identities=19%  Similarity=0.294  Sum_probs=45.2

Q ss_pred             CCCCccccCCCCeEeecCCCCCHHHHHHHhhcC------------------CChhHHHHHHHhcCCCHHHHHHHHHH---
Q psy938           17 ESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT------------------KDSEVYDLLKLFSFDSLAAIEDFKRQ---   75 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~------------------~D~~v~~~l~~~t~l~~eei~~i~~~---   75 (241)
                      ++++|||||.||+.-|+.   +-+.|=--=+++                  .|.-|   |++||.  .+=++++++.   
T Consensus       706 LNsEKMSKSTGNfmTL~q---aieKFgad~tRlalAdaGD~veDANF~ea~AnAaI---LRLyt~--~ew~eEm~~~~s~  777 (1080)
T KOG0437|consen  706 LNSEKMSKSTGNFMTLEQ---AIEKFGADGTRLALADAGDGVEDANFVEANANAAI---LRLYTY--VEWIEEMCENRSS  777 (1080)
T ss_pred             ecchhhccccCCeeeHHH---HHHHhCccceeeeeecccCCcccchhHHhcccHHH---HHHHHH--HHHHHHHHhhHHh
Confidence            356899999999988876   443332222222                  22333   444442  2335555543   


Q ss_pred             hhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           76 NEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        76 ~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      .+.||...-+-+.++.++..++.-.+
T Consensus       778 LrtGp~~~FaDrvf~nemN~~i~~t~  803 (1080)
T KOG0437|consen  778 LRTGPASTFADRVFENEMNALIAKTE  803 (1080)
T ss_pred             hccCchhhHHHHHHHHHHHHHHHHHH
Confidence            34566555788889999887765433

>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase

Probab=90.90  E-value=0.1  Score=49.02  Aligned_cols=30  Identities=20%  Similarity=0.110  Sum_probs=22.6

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeec
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      .+++.+...++....|.|||||.||.|.++
T Consensus       258 ~~P~~~~ye~V~l~gg~KMSKSkGnvI~~~  287 (353)
T cd00674         258 EPPVPVMYEFIGLKGGGKMSSSKGNVITPS  287 (353)
T ss_pred             CCCeEEEeeeEEeCCCCccCCCCCCcCCHH
Confidence            445667777776555679999999998665

Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.

>PLN02959 aminoacyl-tRNA ligase

Probab=90.63  E-value=0.085  Score=56.26  Aligned_cols=21  Identities=29%  Similarity=0.221  Sum_probs=17.3

Q ss_pred             ccccCCCCCccccCCCCeEeec
Q psy938           12 PIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      .++. .+|+|||||.||.|++.
T Consensus       710 G~V~-~~G~KMSKSkGNvI~p~  730 (1084)
T PLN02959        710 GHLM-LNSEKMSKSTGNFLTLR  730 (1084)
T ss_pred             cEEe-cCCcCccccCCCcCCHH
Confidence            3444 79999999999999875

>PRK14536 cysS cysteinyl-tRNA synthetase; Provisional

Probab=90.48  E-value=0.074  Score=52.06  Aligned_cols=19  Identities=32%  Similarity=0.200  Sum_probs=16.7

Q ss_pred             CCCCCccccCCCCeEeecC
Q psy938           16 SESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~   34 (241)
                      ..+|+|||||.||.|+|.+
T Consensus       274 ~~~g~KMSKSlGN~itl~d  292 (490)
T PRK14536        274 LMNKGKMSKSAGQFLTLSS  292 (490)
T ss_pred             eecCccccccCCCcccHHH
Confidence            4689999999999999863

>KOG4655|consensus

Probab=90.39  E-value=0.13  Score=43.39  Aligned_cols=40  Identities=23%  Similarity=0.159  Sum_probs=35.8

Q ss_pred             HHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          152 LSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       152 lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++...+++.|-.+|-++|+||-|+|+-..|+||.+.++.+
T Consensus       112 Vm~~l~m~~~~k~A~~~vEqGHVRvGp~~vtDPa~lvtr~  151 (181)
T KOG4655|consen  112 VMGRLRMAESVKEAVRFVEQGHVRVGPKVVTDPAFLVTRS  151 (181)
T ss_pred             eeeechhhhhHHHHHHHHHcCceeeCCeeccCchHHhhhh
Confidence            4556789999999999999999999999999999988744

>PRK11025 23S rRNA pseudouridylate synthase C; Provisional

Probab=90.16  E-value=0.54  Score=43.23  Aligned_cols=46  Identities=15%  Similarity=0.124  Sum_probs=36.6

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+.+|.++|.......|++.++++|++|.|+|||.++ .++..+...
T Consensus        18 ~g~RLd~~L~~~~~~~sr~~i~~li~~G~V~VNg~~v-~~~~~v~~G   63 (317)
T PRK11025         18 AGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRI-KPEYKLEAG   63 (317)
T ss_pred             CCchHHHHHHHhcccCCHHHHHHHHHcCCEEECCEEc-CcccccCCC
Confidence            3688999998654445999999999999999999987 466655443

>KOG0436|consensus

Probab=90.04  E-value=0.15  Score=49.08  Aligned_cols=24  Identities=38%  Similarity=0.537  Sum_probs=20.4

Q ss_pred             CCCCCccccCCCCeEeecCCCCCHHHHHHHh
Q psy938           16 SESGEKFGKSARNAIWLDSKLSSSFELYQYL   46 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~   46 (241)
                      +-+|.|||||.||.|       +|+++-|+.
T Consensus       339 t~ngmKMsKSLGNvv-------dP~~l~~ky  362 (578)
T KOG0436|consen  339 TKNGMKMSKSLGNVV-------DPFELVQKY  362 (578)
T ss_pred             eecceecchhhcccc-------CHHHHHHHh
Confidence            347999999999997       788888875

>PTZ00399 cysteinyl-tRNA-synthetase; Provisional

Probab=90.03  E-value=0.083  Score=53.43  Aligned_cols=35  Identities=17%  Similarity=0.134  Sum_probs=24.8

Q ss_pred             cCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938           15 ESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus        15 ~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ...+|+|||||.||.|.+.+  ++-+|..++=++++.
T Consensus       309 L~i~G~KMSKSLGNfItp~dlLekygaDaLR~~lLs~  345 (651)
T PTZ00399        309 LHIKGLKMSKSLKNFITIRQALSKYTARQIRLLFLLH  345 (651)
T ss_pred             EEeccchhhhcCCCcccHHHHHHHcChHHHHHHHHhc
Confidence            35799999999999998873  123566666556543

>PRK01611 argS arginyl-tRNA synthetase; Reviewed

Probab=90.00  E-value=0.16  Score=49.71  Aligned_cols=26  Identities=23%  Similarity=0.337  Sum_probs=22.5

Q ss_pred             eecccccCCCCCccccCCCCeEeecC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      ..+.++.+.+|+|||||.||+|++++
T Consensus       310 ~~~glv~~~~g~KMSkR~Gn~i~l~d  335 (507)
T PRK01611        310 QMVGLVRGGEGVKMSTRAGNVVTLDD  335 (507)
T ss_pred             EEEEeeECCCCCcccCCCCceeEHHH
Confidence            34568889999999999999998885

>cd00808 GluRS_core catalytic core domain of discriminating glutamyl-tRNA synthetase

Probab=89.93  E-value=0.29  Score=43.64  Aligned_cols=44  Identities=20%  Similarity=0.159  Sum_probs=31.7

Q ss_pred             ceeeecccccCCCCCccccCCCCe-E-eecCCCCCHHHHHHHhhcC
Q psy938            6 DGGLTTPIIESESGEKFGKSARNA-I-WLDSKLSSSFELYQYLIRT   49 (241)
Q Consensus         6 ~~~lt~pLL~g~dG~KmsKS~gn~-I-~L~~~~Tsp~~~yq~~~~~   49 (241)
                      +.-...|+|++.+|.||||+.|+. | ++-+.-.+|..+..|+..+
T Consensus       147 p~~~h~pll~~~~g~KLSKR~~~~~l~~lr~~G~~p~ai~~~l~~l  192 (239)
T cd00808         147 PKFAHLPLILNPDGKKLSKRKGDTSISDYREEGYLPEALLNYLALL  192 (239)
T ss_pred             CceEeeccccCCCCCcccCCCCCccHHHHHHCCCCHHHHHHHHHHc
Confidence            444588999999999999999982 2 3323334677777777654

Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

>PRK14534 cysS cysteinyl-tRNA synthetase; Provisional

Probab=89.68  E-value=0.088  Score=51.45  Aligned_cols=19  Identities=32%  Similarity=0.220  Sum_probs=16.6

Q ss_pred             CCCCCccccCCCCeEeecC
Q psy938           16 SESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~   34 (241)
                      ..+|+|||||.||.|+|.+
T Consensus       274 ~~~g~KMSKSlGN~i~l~d  292 (481)
T PRK14534        274 IMEYEKMSKSNNNFITIKD  292 (481)
T ss_pred             EecCceecccCCCcccHHH
Confidence            3589999999999999974

>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]

Probab=87.29  E-value=1.6  Score=39.81  Aligned_cols=45  Identities=24%  Similarity=0.226  Sum_probs=37.7

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+.++..+|.+... -|+++..++|.+|.|.|||+++. +++.+..+
T Consensus        11 ~g~rld~~L~~l~~-~sr~~~~~~i~~g~v~vNg~~v~-~~~~l~~g   55 (289)
T COG0564          11 AGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVK-PSYKLKPG   55 (289)
T ss_pred             cCCCHHHHHHHccC-cCHHHHHHHHHCCCEEECCEEcc-CCeeeCCC
Confidence            36789999988433 59999999999999999999998 77777654

>KOG2007|consensus

Probab=85.76  E-value=1.4  Score=43.46  Aligned_cols=33  Identities=30%  Similarity=0.274  Sum_probs=26.9

Q ss_pred             CCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938           17 ESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      .+|+|||||.+|+|-+-+  ++-||.+++=+|+..
T Consensus       301 i~g~KMSKSLkNFiTIke~Lk~~sp~qLRl~fl~~  335 (586)
T KOG2007|consen  301 INGEKMSKSLKNFITIKEALKKYSPRQLRLAFLLH  335 (586)
T ss_pred             eccchhhhhhccceeHHHHHHhcCHHHHHHHHHHH
Confidence            478999999999988762  456899999888775

>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6

Probab=85.74  E-value=1.8  Score=40.98  Aligned_cols=31  Identities=16%  Similarity=0.107  Sum_probs=7.4

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeec
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      ..+++++.--++..-.|+|||||.||.|-+.
T Consensus       264 ~~pP~~~~YE~~~~~g~~kmSsSkG~~~t~~  294 (360)
T PF01921_consen  264 YEPPVPFPYEFFLDKGGGKMSSSKGNGITPE  294 (360)
T ss_dssp             ----EEEEE--EEES--------------HH
T ss_pred             CCCCCCCCeeEEEeCCCcccccCCCCccCHH
Confidence            4466677766777777789999999987554

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.

>KOG3301|consensus

Probab=85.58  E-value=0.7  Score=38.99  Aligned_cols=44  Identities=11%  Similarity=0.044  Sum_probs=38.1

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP  190 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~  190 (241)
                      .+|...+.++|+++|-..||-+|.++.|.|+++.|.-|.+.+..
T Consensus        97 rRLqt~vFklGlAkSIhhARvLi~~rhI~V~~qiV~IPsf~vrl  140 (183)
T KOG3301|consen   97 RRLQTIVFKLGLAKSIHHARVLIRQRHIRVGKQIVNIPSFMVRL  140 (183)
T ss_pred             HHHHHHHHHHhhhhhhHHHHHHhcCccEEecCeEeeccceeEee
Confidence            34666778899999999999999999999999999888877653

>COG0495 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]

Probab=85.04  E-value=0.53  Score=48.80  Aligned_cols=38  Identities=21%  Similarity=0.267  Sum_probs=24.1

Q ss_pred             ccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938           12 PIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      -.+.+.+|+|||||.||.|-+++  ++-.++..+=|+|.+
T Consensus       570 GmVl~~~g~KMSKSKgN~v~p~~~i~~yGADt~Rl~~m~~  609 (814)
T COG0495         570 GMVLGEEGEKMSKSKGNVVDPEEAVEKYGADTVRLYIMFA  609 (814)
T ss_pred             ceEEecCCCccccccCCCCCHHHHHHHhCchHHHHHHHhh
Confidence            34555589999999999996663  111233444455554

>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete

Probab=84.78  E-value=0.38  Score=47.46  Aligned_cols=18  Identities=22%  Similarity=0.316  Sum_probs=14.8

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      -+|+|||||.||.|.+++
T Consensus       270 ~~g~KMSKS~Gn~itl~d  287 (515)
T TIGR00467       270 GKGGKMSSSKGDVISVKD  287 (515)
T ss_pred             CCCccccCCCCCCccHHH
Confidence            357899999999997763

This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.

>PLN02563 aminoacyl-tRNA ligase

Probab=84.40  E-value=0.86  Score=48.24  Aligned_cols=14  Identities=36%  Similarity=0.363  Sum_probs=11.6

Q ss_pred             CccccCCCCeEeec
Q psy938           20 EKFGKSARNAIWLD   33 (241)
Q Consensus        20 ~KmsKS~gn~I~L~   33 (241)
                      +|||||.||.|+.+
T Consensus       722 eKMSKSKGNvVdP~  735 (963)
T PLN02563        722 HKMSKSRGNVVNPD  735 (963)
T ss_pred             cccccccCCcCCHH
Confidence            39999999998544

>KOG0433|consensus

Probab=82.56  E-value=0.73  Score=47.24  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=18.0

Q ss_pred             eecccccCCCCCccccCCCCeE
Q psy938            9 LTTPIIESESGEKFGKSARNAI   30 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I   30 (241)
                      +|.--..+..|.|||||.||.|
T Consensus       601 ivHGFtlDE~G~KMSKSlGNVi  622 (937)
T KOG0433|consen  601 IVHGFTLDENGNKMSKSLGNVV  622 (937)
T ss_pred             eeeeeEecCCccchhhcccCcC
Confidence            4455567889999999999987

>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family

Probab=80.05  E-value=0.5  Score=49.23  Aligned_cols=28  Identities=29%  Similarity=0.234  Sum_probs=17.9

Q ss_pred             ccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           21 KFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        21 KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      |||||.||.|.+++  ++-.++.++=+++.
T Consensus       604 KMSKS~GN~v~p~~ii~~ygaDalRl~~l~  633 (842)
T TIGR00396       604 KMSKSKGNGIDPQEIVKKHGADALRLYIMF  633 (842)
T ss_pred             hhhhcCCCcCCHHHHHHHcCchHHHHHHHh
Confidence            99999999997652  11234455555553

The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	241
2ts1_A	419	Structure Of Tyrosyl-TRNA SYNTHETASE REFINED AT 2.3		2e-27
1jii_A	420	Crystal Structure Of S. Aureus Tyrrs In Complex Wit		6e-27
2pid_A	356	Crystal Structure Of Human Mitochondrial Tyrosyl-tr		5e-24
2jan_A	432	Tyrosyl-Trna Synthetase From Mycobacterium Tubercul		6e-23
1wq3_A	322	Escherichia Coli Tyrosyl-Trna Synthetase Mutant Com		6e-21
1wq4_A	321	Escherichia Coli Tyrosyl-Trna Synthetase Mutant Com		6e-21
1x8x_A	322	Tyrosyl T-Rna Synthetase From E.Coli Complexed With		6e-21
1vbn_A	318	Escherichia Coli Tyrosyl-Trna Synthetase Mutant Com		6e-21
1vbm_A	318	Crystal Structure Of The Escherichia Coli Tyrosyl-T		7e-21
1tyc_A	319	Structural Analysis Of A Series Of Mutants Of Tyros		1e-19
1tyd_E	319	Structure Of Tyrosyl-Trna Synthetase Refined At 2.3		2e-19
1tyb_E	319	Structural Analysis Of A Series Of Mutants Of Tyros		2e-19
1tya_E	319	Structural Analysis Of A Series Of Mutants Of Tyros		2e-19
4ts1_A	319	Crystal Structure Of A Deletion Mutant Of A Tyrosyl		2e-19
1y42_X	392	Crystal Structure Of A C-Terminally Truncated Cyt-1		2e-18

>pdb|2TS1|A Chain A, Structure Of Tyrosyl-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS Resolution. Interaction Of The Enzyme With The Tyrosyl Adenylate Intermediate Length = 419

Iteration: 1
 Score =  119 bits (298), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 71/198 (35%), Positives = 111/198 (56%), Gaps = 9/198 (4%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A   ++AL+S D+ +L      
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRISEALFSGDIANL------ 330
Query: 128 DASRIFPGARIVELLMEPG--MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQ 185
            A+ I  G + V   +  G  + ++EL ++    P  ++A   I  G  YVN +++Q+  
Sbjct: 331 TAAEIEQGFKDVPSFVHEGGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVG 390
Query: 186 EVLSPSAHILPNSLTLLR 203
            +L+ + H L    T++R
Sbjct: 391 AILT-AEHRLEGRFTVIR 407

>pdb|1JII|A Chain A, Crystal Structure Of S. Aureus Tyrrs In Complex With Sb-219383 Length = 420

Iteration: 1
 Score =  117 bits (293), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 68/203 (33%), Positives = 104/203 (51%), Gaps = 19/203 (9%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G+KFGKS   A+WLD++ +S +E YQ+ I   D +V   LK F+F    
Sbjct: 218 GLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKE 277
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I+  ++     P  R AQK LAE++T  +HGE+ L  A   +QAL+S DL SL +    
Sbjct: 278 EIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALFSGDLKSLSAKELK 337
Query: 128 DASRIFP-------GARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKK 180
           D  +  P          IVE+L+E G+S           P  ++A   ++ G  Y+N ++
Sbjct: 338 DGFKDVPQVTLSNDTTNIVEVLIETGIS-----------PSKRQAREDVNNGAIYINGER 386
Query: 181 VQNPQEVLSPSAHILPNSLTLLR 203
            Q+    L+P   I     T++R
Sbjct: 387 QQDVNYALAPEDKI-DGEFTIIR 408

>pdb|2PID|A Chain A, Crystal Structure Of Human Mitochondrial Tyrosyl-trna Synthetase In Complex With An Adenylate Analog Length = 356

Iteration: 1
 Score =  107 bits (268), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 54/109 (49%), Positives = 71/109 (65%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T P+I S +G K GKSA NA+WL+   +S FELYQ+ +R  D  V   LKLF+F  L 
Sbjct: 241 GITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLP 300
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQ 116
            I+   + +  +PE R  QK+LA ++T LVHG EGL SAK  TQALY +
Sbjct: 301 EIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQALYHR 349

>pdb|2JAN|A Chain A, Tyrosyl-Trna Synthetase From Mycobacterium Tuberculosis In Unliganded State Length = 432

Iteration: 1
 Score =  103 bits (258), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 68/205 (33%), Positives = 110/205 (53%), Gaps = 21/205 (10%)
Query: 9   LTTPIIESESGEKFGKS-ARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           LT P++ +  G KFGKS    ++WLD +++S +  YQY + T D++V   L+ F+F S  
Sbjct: 219 LTVPLVTAADGTKFGKSTGGGSLWLDPQMTSPYAWYQYFVNTADADVIRYLRWFTFLSAD 278
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD----LDS--- 120
            + + ++    +P++R AQ++LA +LT+LVHGE    + + A++AL+ +     LD    
Sbjct: 279 ELAELEQATAQRPQQRAAQRRLASELTVLVHGEAATAAVEHASRALFGRGELARLDEATL 338
Query: 121 LGSLNATDASRIFPGA--RIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNY 178
             +L  T  + + PG+   IV+LL+  G+S      A+K   R      TI EGG  VN 
Sbjct: 339 AAALRETTVAELKPGSPDGIVDLLVASGLS------ASKGAARR-----TIHEGGVSVNN 387
Query: 179 KKVQNPQEVLSPSAHILPNSLTLLR 203
            +V N + V   S  +    L L R
Sbjct: 388 IRVDNEEWVPQSSDFLHGRWLVLRR 412

>pdb|1WQ3|A Chain A, Escherichia Coli Tyrosyl-Trna Synthetase Mutant Comlexed With 3-Iodo- L-Tyrosine Length = 322

Iteration: 1
 Score = 97.4 bits (241), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 66/100 (66%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 222 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 281
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 282 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 321

>pdb|1WQ4|A Chain A, Escherichia Coli Tyrosyl-Trna Synthetase Mutant Complexed With L- Tyrosine Length = 321

Iteration: 1
 Score = 97.4 bits (241), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 66/100 (66%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 221 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 280
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 281 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 320

>pdb|1X8X|A Chain A, Tyrosyl T-Rna Synthetase From E.Coli Complexed With Tyrosine Length = 322

Iteration: 1
 Score = 97.4 bits (241), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 66/100 (66%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 222 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 281
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 282 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 321

>pdb|1VBN|A Chain A, Escherichia Coli Tyrosyl-Trna Synthetase Mutant Complexed With Tyr-Ams Length = 318

Iteration: 1
 Score = 97.4 bits (241), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 66/100 (66%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 218 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 277
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 278 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 317

>pdb|1VBM|A Chain A, Crystal Structure Of The Escherichia Coli Tyrosyl-Trna Synthetase Complexed With Tyr-Ams Length = 318

Iteration: 1
 Score = 97.4 bits (241), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 66/100 (66%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 218 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 277
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 278 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 317

>pdb|1TYC|A Chain A, Structural Analysis Of A Series Of Mutants Of Tyrosyl-Trna Synthetase: Enhancement Of Catalysis By Hydrophobic Interactions Length = 319

Iteration: 1
 Score = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA 106
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQA 315

>pdb|1TYD|E Chain E, Structure Of Tyrosyl-Trna Synthetase Refined At 2.3 Angstroms Resolution. Interaction Of The Enzyme With The Tyrosyl Adenylate Intermediate Length = 319

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA 106
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQA 315

>pdb|1TYB|E Chain E, Structural Analysis Of A Series Of Mutants Of Tyrosyl-Trna Synthetase: Enhancement Of Catalysis By Hydrophobic Interactions Length = 319

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA 106
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQA 315

>pdb|1TYA|E Chain E, Structural Analysis Of A Series Of Mutants Of Tyrosyl-Trna Synthetase: Enhancement Of Catalysis By Hydrophobic Interactions Length = 319

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA 106
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQA 315

>pdb|4TS1|A Chain A, Crystal Structure Of A Deletion Mutant Of A Tyrosyl-TRNA Synthetase Complexed With Tyrosine Length = 319

Iteration: 1
 Score = 92.8 bits (229), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 62/99 (62%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSA 106
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQA 315

>pdb|1Y42|X Chain X, Crystal Structure Of A C-Terminally Truncated Cyt-18 Protein Length = 392

Iteration: 1
 Score = 89.4 bits (220), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/111 (39%), Positives = 66/111 (59%)
Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G T P++   SG KFGKSA NAIWLD   +S F+ Y Y +R  D EV +LLKLF+F  ++
Sbjct: 280 GFTVPLLTDSSGAKFGKSAGNAIWLDPYQTSVFDFYGYFVRRSDQEVENLLKLFTFMPIS 339
Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDL 118
            I     ++   P +R AQ  LA ++  LVHG++   +A+   + +Y+  +
Sbjct: 340 EITKTMEEHIKDPSKRVAQHTLAREVVTLVHGKQEASAAEDQHRMMYTGQM 390

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	241
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	4e-50
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	7e-50
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	1e-49
2pid_A	356	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	8e-44
1y42_X	392	Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tR	2e-43
2yxn_A	322	Tyrosyl-tRNA synthetase; tRNA synthetases class I,	4e-35
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	2e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A Length = 419

 Score =  167 bits (426), Expect = 4e-50
 Identities = 68/196 (34%), Positives = 106/196 (54%), Gaps = 5/196 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A   ++AL+S D+    +L A 
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRISEALFSGDIA---NLTAA 333

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +  + F             + ++EL ++    P  ++A   I  G  YVN +++Q+   +
Sbjct: 334 EIEQGFKDVPSFVHEGG-DVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAI 392

Query: 188 LSPSAHILPNSLTLLR 203
           L+   H L    T++R
Sbjct: 393 LTAE-HRLEGRFTVIR 407

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Length = 420

 Score =  167 bits (425), Expect = 7e-50
 Identities = 64/196 (32%), Positives = 104/196 (53%), Gaps = 5/196 (2%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G+KFGKS   A+WLD++ +S +E YQ+ I   D +V   LK F+F    
Sbjct: 218 GLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKE 277

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNAT 127
            I+  ++     P  R AQK LAE++T  +HGE+ L  A   +QAL+S DL    SL+A 
Sbjct: 278 EIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALFSGDLK---SLSAK 334

Query: 128 DASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEV 187
           +    F     V L  +   +++E+ + T   P  ++A   ++ G  Y+N ++ Q+    
Sbjct: 335 ELKDGFKDVPQVTLSND-TTNIVEVLIETGISPSKRQAREDVNNGAIYINGERQQDVNYA 393

Query: 188 LSPSAHILPNSLTLLR 203
           L+P    +    T++R
Sbjct: 394 LAPE-DKIDGEFTIIR 408

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Length = 432

 Score =  167 bits (424), Expect = 1e-49
 Identities = 59/197 (29%), Positives = 102/197 (51%), Gaps = 4/197 (2%)

Query: 8   GLTTPIIESESGEKFGKS-ARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSL 66
            LT P++ +  G KFGKS    ++WLD +++S +  YQY + T D++V   L+ F+F S 
Sbjct: 218 ALTVPLVTAADGTKFGKSTGGGSLWLDPQMTSPYAWYQYFVNTADADVIRYLRWFTFLSA 277

Query: 67  AAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNA 126
             + + ++    +P++R AQ++LA +LT+LVHGE    + + A++AL+ +    L  L+ 
Sbjct: 278 DELAELEQATAQRPQQRAAQRRLASELTVLVHGEAATAAVEHASRALFGR--GELARLDE 335

Query: 127 TDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQE 186
              +       + EL       +++L +A+        A  TI EGG  VN  +V N + 
Sbjct: 336 ATLAAALRETTVAELKPGSPDGIVDLLVASGLSASKGAARRTIHEGGVSVNNIRVDNEEW 395

Query: 187 VLSPSAHILPNSLTLLR 203
           V    +  L     +LR
Sbjct: 396 VPQS-SDFLHGRWLVLR 411

>2pid_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, protein-substrate complex, ATP-BI ligase, mitochondrion, nucleotide-binding, protein biosynth; HET: YSA; 2.20A {Homo sapiens} PDB: 3zxi_A* Length = 356

 Score =  150 bits (380), Expect = 8e-44
 Identities = 54/113 (47%), Positives = 71/113 (62%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G+T P+I S +G K GKSA NA+WL+   +S FELYQ+ +R  D  V   LKLF+F  L 
Sbjct: 241 GITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLP 300

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDS 120
            I+   + +  +PE R  QK+LA ++T LVHG EGL SAK  TQALY +    
Sbjct: 301 EIDHIMQLHVKEPERRGPQKRLAAEVTKLVHGREGLDSAKRCTQALYHRSHHH 353

>1y42_X Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tRNA ligase, group I intron; HET: TYR; 1.95A {Neurospora crassa} PDB: 2rkj_A Length = 392

 Score =  149 bits (379), Expect = 2e-43
 Identities = 44/112 (39%), Positives = 66/112 (58%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           G T P++   SG KFGKSA NAIWLD   +S F+ Y Y +R  D EV +LLKLF+F  ++
Sbjct: 280 GFTVPLLTDSSGAKFGKSAGNAIWLDPYQTSVFDFYGYFVRRSDQEVENLLKLFTFMPIS 339

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLD 119
            I     ++   P +R AQ  LA ++  LVHG++   +A+   + +Y+  + 
Sbjct: 340 EITKTMEEHIKDPSKRVAQHTLAREVVTLVHGKQEASAAEDQHRMMYTGQMT 391

>2yxn_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, structural genomics, NPPSFA, natio project on protein structural and functional analyses; HET: AZY; 1.80A {Escherichia coli str} PDB: 1wq3_A* 1wq4_A* 1x8x_A* 1vbn_A* 1vbm_A* Length = 322

 Score =  126 bits (319), Expect = 4e-35
 Identities = 46/100 (46%), Positives = 66/100 (66%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P+I    G KFGK+   A+WLD K +S ++ YQ+ I T D++VY  LK F+F S+ 
Sbjct: 222 GLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIE 281

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAK 107
            I   + ++++  +  RAQ  LAE +T LVHGEEGL++AK
Sbjct: 282 EINALEEEDKNSGKAPRAQYVLAEQVTRLVHGEEGLQAAK 321

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Length = 432

 Score = 88.2 bits (219), Expect = 2e-20
 Identities = 34/208 (16%), Positives = 60/208 (28%), Gaps = 28/208 (13%)

Query: 8   GLTTPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSL 66
               P++    G EK  KS  N I L         +++ L+R  D  +    +L +    
Sbjct: 218 CFLMPLLVGLDGREKMSKSLDNYIGLTE---PPEAMFKKLMRVPDPLLPSYFRLLTDLEE 274

Query: 67  AAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNA 126
             IE   +          A + LA  LT      +       A         ++ G    
Sbjct: 275 EEIEALLKAG-----PVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKE 329

Query: 127 TDA----------SRIFPGARIVEL---------LMEPGMSMLELSLATKCFPRDKEANL 167
                          +  G    E+         L E  + +  L       P + EA  
Sbjct: 330 AGPEEVRRAEARYDEVAKGGIPEEIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARR 389

Query: 168 TISEGGFYVNYKKVQNPQEVLSPSAHIL 195
            I   G  ++ + + +P   +  S   +
Sbjct: 390 LIQNRGLRLDGEVLTDPMLQVDLSRPRI 417

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 45.2 bits (106), Expect = 1e-05
 Identities = 42/235 (17%), Positives = 82/235 (34%), Gaps = 64/235 (27%)

Query: 50  KDSEVYDLLKLFSFDSLAAI---EDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKS- 105
            + +  D+      D   +I   E+       K       +      TLL   EE ++  
Sbjct: 31  DNFDCKDVQ-----DMPKSILSKEEIDHIIMSKDAVSGTLRLFW---TLLSKQEEMVQKF 82

Query: 106 -------------AKLATQ--------ALYSQDLDSLGSLNAT----DASRIFPGARIVE 140
                        + + T+         +Y +  D L + N      + SR+ P  ++ +
Sbjct: 83  VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142

Query: 141 LLME--P-------GM-----SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQE 186
            L+E  P       G+     + + L +         +    +    F++N K   +P+ 
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALDVC-----LSYKVQCKMDFKIFWLNLKNCNSPET 197

Query: 187 VLSP----SAHILPNSLTLLRVEVSANIIAKSANIIAKSANIIAKSHRY-DMYIV 236
           VL         I PN  +  R + S+NI  +  +I A+   ++ KS  Y +  +V
Sbjct: 198 VLEMLQKLLYQIDPNWTS--RSDHSSNIKLRIHSIQAELRRLL-KSKPYENCLLV 249

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	241
2jan_A	432	Tyrosyl-tRNA synthetase; protein biosynthesis, ami	100.0
2ts1_A	419	Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30	100.0
1jil_A	420	Tyrrs, tyrosyl-tRNA synthetase; truncation, based	100.0
1h3f_A	432	Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy	100.0
1y42_X	392	Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tR	99.96
2pid_A	356	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	99.96
2yxn_A	322	Tyrosyl-tRNA synthetase; tRNA synthetases class I,	99.93
1n3l_A	372	Tyrosyl-tRNA synthetase; rossmann fold AS catalyti	99.8
2el7_A	337	Tryptophanyl-tRNA synthetase; aminoacyl-tRNA synth	99.78
2dlc_X	394	Tyrosyl-tRNA synthetase, cytoplasmic; tyrrs, ligas	99.76
2g36_A	340	Tryptophanyl-tRNA synthetase; TM0492, structural g	99.75
3tzl_A	322	Tryptophanyl-tRNA synthetase; structural genomics,	99.73
1yi8_B	351	Tryptophanyl-tRNA synthetase; ligase; HET: TRP; 2.	99.71
2cya_A	364	Tyrosyl-tRNA synthetase; tyrrs, aminoacylation, st	99.71
2ktl_A	164	Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA s	99.7
2cyc_A	375	Tyrosyl-tRNA synthetase; tyrosine, tyrrs, aminoacy	99.7
1r6u_A	437	Tryptophanyl-tRNA synthetase; class IC tRNA synthe	99.67
2ip1_A	432	Tryptophanyl-tRNA synthetase; rossmann fold, struc	99.66
2zp1_A	314	Tyrosyl-tRNA synthetase; tRNA synthetases class I,	99.66
1r6t_A	477	Tryptophanyl-tRNA synthetase; class IC tRNA synthe	99.65
2cyb_A	323	Tyrosyl-tRNA synthetase; rossmann-fold, structural	99.63
3hzr_A	386	Tryptophanyl-tRNA synthetase; APO tRNA-ligase, str	99.59
1i6k_A	328	TRPRS, tryptophanyl-tRNA synthetase; class I tRNA	99.58
3jxe_A	392	Tryptophanyl-tRNA synthetase; adenosine triphospha	99.56
3hv0_A	393	Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-bin	99.56
3i05_A	395	Tryptophanyl-tRNA synthetase; APO tRNA-ligase, ATP	99.55
3tze_A	406	Tryptophanyl-tRNA synthetase; structural genomics,	99.54
2j5b_A	348	Tyrosyl-tRNA synthetase; ligase, protein biosynthe	99.54
2yy5_A	348	Tryptophanyl-tRNA synthetase; aminoaccyl tRNA synt	99.53
3vgj_A	373	Tyrosyl-tRNA synthetase, putative; tyrrs, ligase;	99.48
3p0j_A	690	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	99.47
3foc_A	451	Tryptophanyl-tRNA synthetase; structural genomics,	99.38
3a04_A	372	Tryptophanyl-tRNA synthetase; ligase, aminoacyl-tR	99.22
3sz3_A	341	Tryptophanyl-tRNA synthetase; structural genomics,	99.18
3prh_A	388	Tryptophanyl-tRNA synthetase; TRPRS, protein biosy	99.17
3n9i_A	346	Tryptophanyl-tRNA synthetase; tryptophan-tRNA liga	99.17
1p9k_A	79	ORF, hypothetical protein; alfal motif, RNA-bindin	98.54
3p0j_A	690	Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase	98.53
2cqj_A	71	BRMS2, U3 small nucleolar ribonucleoprotein protei	98.19
3j20_D	180	30S ribosomal protein S4P; archaea, archaeal, KINK	97.76
1c05_A	159	Ribosomal protein S4 delta 41; two subdomains, uni	97.71
3u5c_J	197	40S ribosomal protein S9-A; translation, ribosome,	97.69
2xzm_D	181	Ribosomal protein S4 containing protein; ribosome,	97.58
2vqe_D	209	30S ribosomal protein S4; tRNA-binding, rRNA-bindi	97.25
1dm9_A	133	Hypothetical 15.5 KD protein in MRCA-PCKA intergen	97.24
3r8n_D	205	30S ribosomal protein S4; protein biosynthesis, RN	97.01
3bbn_D	201	Ribosomal protein S4; small ribosomal subunit, spi	96.93
3hp7_A	291	Hemolysin, putative; structural genomics, APC64019	96.86
2k6p_A	92	Uncharacterized protein HP_1423; alpha-L motif, RN	96.69
3iz6_C	195	40S ribosomal protein S9 (S4P); eukaryotic ribosom	96.41
3dh3_A	290	Ribosomal large subunit pseudouridine synthase F;	96.3
1ksk_A	234	Ribosomal small subunit pseudouridine synthase A;	95.85
1vio_A	243	Ribosomal small subunit pseudouridine synthase A;	95.43
3j20_E	243	30S ribosomal protein S4E; archaea, archaeal, KINK	95.34
2d5b_A	500	Methionyl-tRNA synthetase; rossmann fold, class 1A	95.26
1irx_A	523	Lysyl-tRNA synthetase; beta sandwitch, zinc-bindin	94.76
3kbg_A	213	30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2	94.71
3u1f_A	542	Methionyl-tRNA synthetase; aminoacyl-tRNA syntheta	94.54
1gax_A	862	Valrs, valyl-tRNA synthetase; protein-RNA complex,	94.49
2csx_A	497	Methionyl-tRNA synthetase; ligase, riken structura	94.44
1v9f_A	325	Ribosomal large subunit pseudouridine synthase D;	93.84
1ile_A	821	Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA s	93.84
1ffy_A	917	Isoleucyl-tRNA synthetase; protein-RNA complex, me	93.45
3kfl_A	564	Methionyl-tRNA synthetase; parasite, aminoacyl-tRN	93.14
4dlp_A	536	Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA	93.11
1li5_A	461	Cysrs, cysteinyl-tRNA synthetase, transfer RNA-Cys	93.1
3c8z_A	414	Cysteinyl-tRNA synthetase; cysteine ligase, rossma	93.03
3tqo_A	462	Cysteinyl-tRNA synthetase; protein synthesis, liga	92.86
2x1l_A	524	Methionyl-tRNA synthetase; nucleotide-binding, pro	92.63
1rqg_A	722	Methionyl-tRNA synthetase; translation, dimerizati	92.57
1wkb_A	810	Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, e	92.56
3h99_A	560	Methionyl-tRNA synthetase; rossmann fold, aminoacy	92.51
1wz2_A	967	Leucyl-tRNA synthetase; ligase, riken structural g	92.41
3sp1_A	501	Cysteinyl-tRNA synthetase; structural genomics, se	92.12
1nzj_A	298	Hypothetical protein YADB; Zn cluster, glutamyl T-	90.07
2cfo_A	492	Glutamyl-tRNA synthetase; ligase, aminoacyl-tRNA s	89.93
3iz6_D	265	40S ribosomal protein S4 (S4E); eukaryotic ribosom	89.63
2xzm_W	260	40S ribosomal protein S4; ribosome, translation; 3	88.17
3fnr_A	464	Arginyl-tRNA synthetase; transferase, PSI-2, NYSGX	83.97
3u5c_E	261	RP5, S7, YS6, 40S ribosomal protein S4-A; translat	83.74
4arc_A	880	Leucine--tRNA ligase; ligase-RNA complex, nucleoti	82.44
4g6z_A	490	Glutamate-tRNA ligase; aminoacyl-tRNA synthetase,	81.97
2v0c_A	878	Aminoacyl-tRNA synthetase; ligase, nucleotide-bind	81.17
3al0_C	592	Glutamyl-tRNA(Gln) amidotransferase subunit C, GL	80.35

>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}

Probab=100.00  E-value=5.8e-52  Score=391.54  Aligned_cols=209  Identities=30%  Similarity=0.507  Sum_probs=194.1

Q ss_pred             CCCceeeecccccCCCCCccccCCCC-eEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARN-AIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE   81 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~   81 (241)
                      ..+++++|+|+|||+||+|||||++| +|||+++||||+++||||+|++|++|.+|+++||+++.++|+++++++..+++
T Consensus       213 ~~~~~~l~~plL~~ldG~KMSKS~~nsaI~L~d~~tsp~~i~qki~~~~D~~v~~~l~l~t~~~~~ei~~l~~~~~~g~~  292 (432)
T 2jan_A          213 GATVHALTVPLVTAADGTKFGKSTGGGSLWLDPQMTSPYAWYQYFVNTADADVIRYLRWFTFLSADELAELEQATAQRPQ  292 (432)
T ss_dssp             CCCCEEEECCCCBCTTSCBTTBCSSSCBCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHSCCCHHHHHHHHHHHHHCGG
T ss_pred             CCCccccccccccCCCcCcCCCCCCCCeEEccCCCCCHHHHHHHHhcCCchhHHHHHHHHHcCChHHHHHHHHHHhhccC
Confidence            35799999999999999999999999 99999999999999999999999999999999999999999999999988889


Q ss_pred             hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCC--cHHHHHHhcCCC
Q psy938           82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGM--SMLELSLATKCF  159 (241)
Q Consensus        82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~--~l~~lLv~~gl~  159 (241)
                      ++++|+.||++|++++||++++++|+++++++|+.+  ++..++++++++.+.++|.+++.  .+.  ++.++|+.+|++
T Consensus       293 ~~~~K~~LA~~v~~~~hg~~~~~~a~~~~~~lf~~~--~~~~l~~~~~~~~~~~~p~~~~~--~~~~~~~~~ll~~~gl~  368 (432)
T 2jan_A          293 QRAAQRRLASELTVLVHGEAATAAVEHASRALFGRG--ELARLDEATLAAALRETTVAELK--PGSPDGIVDLLVASGLS  368 (432)
T ss_dssp             GCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSS--CTTSCCHHHHHHHHHHSCEEEEC--SSSCCSHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCC--CcccCCHHHHHHHhccCCeeEec--ccchhhHHHHHHHhCCc
Confidence            999999999999999999999999999999999854  35678889999888889988874  244  799999999999


Q ss_pred             CCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEcc
Q psy938          160 PRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSAN  216 (241)
Q Consensus       160 ~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~~  216 (241)
                      +|++||||+|+||||||||++|+|++..+... +++++++++||+|||+|++|+|..
T Consensus       369 ~S~~earr~i~~ggv~in~~~v~d~~~~~~~~-~~~~~~~~~l~~GKk~~~~v~~~~  424 (432)
T 2jan_A          369 ASKGAARRTIHEGGVSVNNIRVDNEEWVPQSS-DFLHGRWLVLRRGKRSIAGVERIG  424 (432)
T ss_dssp             SSHHHHHHHHTTTCEEESSCEECCTTCCCCGG-GSBTTTEEEEESSSSCEEEEEEC-
T ss_pred             ccHHHHHHHHHhCCEEECCEEccChhcccChh-hccCCcEEEEEeCCeeEEEEEECC
Confidence            99999999999999999999999999988764 788999999999999999999953

>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A

Probab=100.00  E-value=1.6e-52  Score=394.30  Aligned_cols=207  Identities=33%  Similarity=0.527  Sum_probs=104.5

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..++|++|+|+|||+||+|||||+||+|||+++||||+++||||+|++|++|.+|+++||+++.++|+++++++..++++
T Consensus       212 ~~~~~~lt~pll~~ldG~KMSKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~l~t~~~~~ei~~l~~~~~~g~~~  291 (419)
T 2ts1_A          212 EARAFGLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKEEIEALEQELREAPEK  291 (419)
T ss_dssp             --CCEEEEECCCCCTTSCCTTCCSSCCCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCTTS
T ss_pred             CCCeeecccccccCCCcccccCCCCCeEecCCCCCCHHHHHHHHhcCCchhHHHHHHHHHcCCHHHHHHHHHHHHccCCH
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999888899


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD  162 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk  162 (241)
                      +++|+.||++|++++||++++++|+++++++|+++   +..++++++++.+.++|.+++.. .+.++.++|+.+|+++|+
T Consensus       292 ~~~K~~LA~~v~~~~hg~~~~~~a~~~~~~lf~~~---~~~l~~~~~~~~~~~~p~~~~~~-~~~~~~~~l~~~gl~~S~  367 (419)
T 2ts1_A          292 RAAQKTLAEEVTKLVHGEEALRQAIRISEALFSGD---IANLTAAEIEQGFKDVPSFVHEG-GDVPLVELLVSAGISPSK  367 (419)
T ss_dssp             CHHHHHHHHHHHHHHHCHHHHHHHHHHC----------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhccc---ccccCHhHHHHHhccceEEEecC-CcccHHHHHHHhCCCCCH
Confidence            99999999999999999999999999999999863   35677888998888889887742 246899999999999999


Q ss_pred             HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEE
Q psy938          163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKS  214 (241)
Q Consensus       163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~  214 (241)
                      +||||+|+||||||||++|+|++..+... +++++++++||+|||+|++|++
T Consensus       368 ~earr~i~~ggv~in~~~v~d~~~~~~~~-~~~~~~~~~l~~GKk~~~~v~~  418 (419)
T 2ts1_A          368 RQAREDIQNGAIYVNGERLQDVGAILTAE-HRLEGRFTVIRRGKKKYYLIRY  418 (419)
T ss_dssp             ----------------------------------------------------
T ss_pred             HHHHHHHHhCCEEECCEEecCcccccChh-hccCCcEEEEEECCeeEEEEEE
Confidence            99999999999999999999999988764 7788899999999999999986

>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*

Probab=100.00  E-value=3e-52  Score=392.76  Aligned_cols=207  Identities=31%  Similarity=0.530  Sum_probs=109.5

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..+++++|+|+|||+||+|||||+||+|||++++|||+++||||+|++|++|.+|+++||+++.++|+++++++..++++
T Consensus       213 ~~~~~~l~~pll~~ldG~KMSKS~~naI~L~d~~tsp~~i~~ki~~~~D~~v~~~l~~~t~~~~~ei~~l~~~~~~g~~~  292 (420)
T 1jil_A          213 QTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPHL  292 (420)
T ss_dssp             CCCCEEEEECCCBCTTSCBTTBCSSSBCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCGGG
T ss_pred             CCCeeEeecccccCCccccccCCCCCeEecCCCCCCHHHHHHHHhcCCchhHHHHHHHHHcCCHHHHHHHHHHHhcCCCh
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999888899


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCH
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRD  162 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~Sk  162 (241)
                      +++|+.||++|++++||++++++|+++++++|+++   +..++++++++.+.++|.+++.. .++++.++|+.+|+++|+
T Consensus       293 ~~~K~~La~~v~~~~hg~~~~~~a~~~~~~~f~~~---~~~~~~~~~~~~~~~~p~~~i~~-~~i~l~~lL~~agl~~Sk  368 (420)
T 1jil_A          293 REAQKTLAEEVTKFIHGEDALNDAIRISQALFSGD---LKSLSAKELKDGFKDVPQVTLSN-DTTNIVEVLIETGISPSK  368 (420)
T ss_dssp             CHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHC------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCC---cccCCHHHHHHHhccceEEEecc-CcccHHHHHHHcCCccCH
Confidence            99999999999999999999999999999999864   35688888888888899887742 246899999999999999


Q ss_pred             HHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEE
Q psy938          163 KEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKS  214 (241)
Q Consensus       163 sEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~  214 (241)
                      +||||+|++|||+|||++++|++..+... +++++++++||+|||+|++|+|
T Consensus       369 sEARRlI~~GgV~VNgekv~d~~~~l~~~-dl~~~~~~~l~~GKk~~~~v~~  419 (420)
T 1jil_A          369 RQAREDVNNGAIYINGERQQDVNYALAPE-DKIDGEFTIIRRGKKKYFMVNY  419 (420)
T ss_dssp             ----------------------------------------------------
T ss_pred             HHHHHHHHhCCEEECCEEecccccccCcc-cccCCcEEEEEECCeeEEEEEE
Confidence            99999999999999999999999988865 7888999999999999999986

>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*

Probab=100.00  E-value=1e-41  Score=321.97  Aligned_cols=186  Identities=17%  Similarity=0.176  Sum_probs=163.2

Q ss_pred             CCCCceeeecccccCCCCC-ccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938            2 EVTGDGGLTTPIIESESGE-KFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKP   80 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG~-KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~   80 (241)
                      +..+++++|+|+|||+||. |||||.+|+|||++   ||+++||||++++|+++.+|+++||+++.+||+++.+.     
T Consensus       212 ~~~~~~~lt~pll~gldG~~KMSKS~~n~I~L~d---sp~~i~~Ki~~~~d~~v~~~l~~ft~~~~eei~~~~~~-----  283 (432)
T 1h3f_A          212 GQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTE---PPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKA-----  283 (432)
T ss_dssp             TCCCCEEEEECCCBCTTSSSBCCGGGTCCCBTTS---CHHHHHHHHHTSCGGGHHHHHHHHCCCCHHHHHHHHHH-----
T ss_pred             CCCCceEeecccccCCCCccccCcCCCCeeCCCC---CHHHHHHHHhCCCccHHHHHHHHcCCCCHHHHHHHHhh-----
Confidence            3567899999999999995 99999999999999   99999999999999999999999999999999998865     


Q ss_pred             ChHHHHHHHHHHHHhhcc-----------------------------CHHHHHHHHHHHHHhccCCcccCCCCChhhHhh
Q psy938           81 EERRAQKKLAEDLTLLVH-----------------------------GEEGLKSAKLATQALYSQDLDSLGSLNATDASR  131 (241)
Q Consensus        81 ~~~~~Kk~LA~~i~~~vh-----------------------------G~~~a~~A~~~~~~lF~~~~~~~~~l~~~~l~~  131 (241)
                      +++++|+.||++|++++|                             |+++|++|.++++.+ +.+          ++++
T Consensus       284 ~~~~~K~~LA~~i~~~l~~~~~pirerr~~~~~~~~v~~il~~~~~~g~~~a~~a~~~~~~~-~~~----------~~~~  352 (432)
T 1h3f_A          284 GPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYAWEAFGRDKEAGPEEVRRAEARYDEV-AKG----------GIPE  352 (432)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSSCCSCCSHHHHHHTTCCGGGTTCCTTCSCHHHHHHHHHHHHH-CC--------------C
T ss_pred             ChHHHHHHHHHHHHHHHhcccchHHHHHHHhhchHHHHHHHhhccccCHHHHHHHHHHHHHh-hcC----------CCCc
Confidence            789999999999999999                             999999999999999 432          2222


Q ss_pred             hcCCCceeeeccC----CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccc
Q psy938          132 IFPGARIVELLME----PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVS  207 (241)
Q Consensus       132 ~~~~~p~~~~~~~----~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk  207 (241)
                         ++|.+++...    .+.++.++|+.+|+++|++||||+|+||||||||++|+|++..+..+      +.++||+|||
T Consensus       353 ---~~p~~~~~~~~~~~~~~~~~~~l~~~~l~~S~~earr~i~~ggv~vn~~~v~d~~~~~~~~------~~~~l~~GKk  423 (432)
T 1h3f_A          353 ---EIPEVTIPASELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLS------RPRILQRGKD  423 (432)
T ss_dssp             ---CSCEEEECGGGCBTTEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEECS------SCEEEEETTT
T ss_pred             ---cCceeEecccccccccCcHHHHHHHhCCcccHHHHHHHHHhCCEEECCEEecCccceecCC------CcEEEEeCCe
Confidence               4565555321    14679999999999999999999999999999999999999887643      2379999999


Q ss_pred             cEEEEEEc
Q psy938          208 ANIIAKSA  215 (241)
Q Consensus       208 ~~~~i~~~  215 (241)
                      +|++|++.
T Consensus       424 ~~~~v~~~  431 (432)
T 1h3f_A          424 RFVRVRLS  431 (432)
T ss_dssp             EEEEEEEC
T ss_pred             eEEEEEeC
Confidence            99999875

>1y42_X Tyrosyl-tRNA synthetase, mitochondrial; CYT-18, tRNA ligase, group I intron; HET: TYR; 1.95A {Neurospora crassa} PDB: 2rkj_A

Probab=99.96  E-value=4.9e-30  Score=239.61  Aligned_cols=114  Identities=39%  Similarity=0.661  Sum_probs=110.4

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCChH
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEER   83 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~~   83 (241)
                      .+++++|+|+|||+||+|||||+||+|||++++|||+++||||++++|++|.+|+++||+++.++|++++++|..+++++
T Consensus       276 ~~~~~l~~pll~~ldG~KMSKS~~naI~L~d~~tsp~~i~qki~~~~D~~v~~~l~~ft~l~~~ei~~l~~~~~~g~~~~  355 (392)
T 1y42_X          276 DECVGFTVPLLTDSSGAKFGKSAGNAIWLDPYQTSVFDFYGYFVRRSDQEVENLLKLFTFMPISEITKTMEEHIKDPSKR  355 (392)
T ss_dssp             GSCEEEECCCCBCTTCCBTTBCSSSBCBSSTTTSCHHHHHHHHHTCCTTTHHHHHHHHCCCCHHHHHHHHHHHHHCGGGC
T ss_pred             CCccccccccCcCCchhhccCCCCCeeeccCCCCCHHHHHHHHHcCCchhHHHHHHHHHhCChhHHHHHHHHHhcCCCHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999998888999


Q ss_pred             HHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCC
Q psy938           84 RAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD  117 (241)
Q Consensus        84 ~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~  117 (241)
                      ++|+.||++|++++||.+++++|.++++++|+++
T Consensus       356 ~~K~~LA~~v~~~lhg~~~~~~a~~~~~~~f~~~  389 (392)
T 1y42_X          356 VAQHTLAREVVTLVHGKQEASAAEDQHRMMYTGQ  389 (392)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHHHHHHTSSCCC-
T ss_pred             HHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999999864

>2pid_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, protein-substrate complex, ATP-BI ligase, mitochondrion, nucleotide-binding, protein biosynth; HET: YSA; 2.20A {Homo sapiens} PDB: 3zxi_A*

Probab=99.96  E-value=9.2e-30  Score=235.15  Aligned_cols=115  Identities=47%  Similarity=0.736  Sum_probs=96.2

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..+++++|.|+|||+||+|||||.||+|||++++|||+++||||++++|++|.+|+++||+++.++|+++++++..++++
T Consensus       236 ~~~~~~l~~pll~~ldG~KMSKS~~naI~L~d~~tsp~~i~~ki~~~~D~~v~~~l~~~t~~~~~~i~~l~~~~~~g~~~  315 (356)
T 2pid_A          236 GEDVFGITVPLITSTTGAKLGKSAGNAVWLNRDKTSPFELYQFFVRQPDDSVERYLKLFTFLPLPEIDHIMQLHVKEPER  315 (356)
T ss_dssp             SCCCEEEEECCCC-------------CCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCGGG
T ss_pred             CCCccccccccccCCCcccccCCCCCeeeccCCCCCHHHHHHHHHcCCchhHHHHHHHHHcCCchHHHHHHHHHhcCCCH
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999888899


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCC
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD  117 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~  117 (241)
                      +++|+.||++|++++||.+++++|++++++||+++
T Consensus       316 ~~~K~~La~~v~~~l~g~~~~~~a~~~~~~lf~~~  350 (356)
T 2pid_A          316 RGPQKRLAAEVTKLVHGREGLDSAKRCTQALYHRS  350 (356)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---
T ss_pred             HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999864

>2yxn_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, structural genomics, NPPSFA, natio project on protein structural and functional analyses; HET: AZY; 1.80A {Escherichia coli str} PDB: 1wq3_A* 1wq4_A* 1x8x_A* 1vbn_A* 1vbm_A*

Probab=99.93  E-value=1.7e-26  Score=210.63  Aligned_cols=104  Identities=44%  Similarity=0.759  Sum_probs=100.1

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCChH
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEER   83 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~~   83 (241)
                      .+++++|+|+|||+||+|||||.+|+|||++++|||+++||||++++|++|.+|+++||+++.+++++++++|..+++++
T Consensus       218 ~~~~~l~~pll~gldG~KMSKS~~n~I~L~d~~tsp~~~~~ki~~~~d~~v~~~l~~~~~~~~~~i~~l~~~~~~g~~~~  297 (322)
T 2yxn_A          218 NQVFGLTVPLITKADGTKFGKTEGGAVWLDPKKTSPYKFYQFWINTADADVYRFLKFFTFMSIEEINALEEEDKNSGKAP  297 (322)
T ss_dssp             CCCEEEECCCCBCTTSCBTTEETTEECBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHSSCC
T ss_pred             CCceeeccCccCCCCcccccCCCCCeeeccCCCCCHHHHHHHHhCCCcccHHHHHHHHHcCCHHHHHHHHHHHHcCCCHH
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999998777999


Q ss_pred             HHHHHHHHHHHhhccCHHHHHHHH
Q psy938           84 RAQKKLAEDLTLLVHGEEGLKSAK  107 (241)
Q Consensus        84 ~~Kk~LA~~i~~~vhG~~~a~~A~  107 (241)
                      ++|+.||++|++++||.+++++|+
T Consensus       298 ~~K~~La~~i~~~l~~~~~~~~a~  321 (322)
T 2yxn_A          298 RAQYVLAEQVTRLVHGEEGLQAAK  321 (322)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHhh
Confidence            999999999999999999998875

>1n3l_A Tyrosyl-tRNA synthetase; rossmann fold AS catalytic domain, unique anticodon recognit domain, dimer, ligase; 1.18A {Homo sapiens} SCOP: c.26.1.1 PDB: 1q11_A*

Probab=99.80  E-value=1.7e-20  Score=174.08  Aligned_cols=111  Identities=16%  Similarity=0.179  Sum_probs=93.8

Q ss_pred             CCCceeeecccccCCCCCccccCCCC-eEeecCCCCCHHHHHHHhhc-------CCChhHHHHHHH--------hcC---
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARN-AIWLDSKLSSSFELYQYLIR-------TKDSEVYDLLKL--------FSF---   63 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-------~~D~~v~~~l~~--------~t~---   63 (241)
                      ..+++++++|+|+|+||+|||||.+| +|||++   +|+++||||++       ++|++|.+|+++        ||+   
T Consensus       204 ~~~p~~l~~pll~gldG~KMSKS~~ns~I~L~d---~p~~i~kKi~~A~td~~~~~d~~v~~~lk~~l~~~~~~f~~er~  280 (372)
T 1n3l_A          204 YSKRVHLMNPMVPGLTGSKMSSSEEESKIDLLD---RKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRD  280 (372)
T ss_dssp             CCCCEEEEECCCCCSSCC-------CCSCBTTC---CHHHHHHHHHTCCCCTTCCSSCHHHHHHHHTTGGGTTCEEECCC
T ss_pred             CCCCEEEecCccCCCCcccccCCCCCCeEeccC---CHHHHHHHHHHccCCCCCCCcccHHHHHHHhhhhhhcceeeccc
Confidence            35689999999999999999999999 899999   99999999988       789999999998        664   


Q ss_pred             ------CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCC
Q psy938           64 ------DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD  117 (241)
Q Consensus        64 ------l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~  117 (241)
                            ++.++++++++++..+ ++++++|+.||++|++++||..+..+ ...++.+|++.
T Consensus       281 ~~~g~~~~~~~i~el~~~~~~g~~~~~~~K~~La~~i~~~l~p~r~~~~-~~~~~~lf~~~  340 (372)
T 1n3l_A          281 EKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFN-TPALKKLASAA  340 (372)
T ss_dssp             GGGTCCEEESSHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHHHHHH
T ss_pred             ccccCCCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhHHHHHhc-CHHHHHHHhcc
Confidence                  5667899999999876 89999999999999999999999888 88899999853

>2el7_A Tryptophanyl-tRNA synthetase; aminoacyl-tRNA synthetase, translation, structural GEN NPPSFA; 2.50A {Thermus thermophilus}

Probab=99.78  E-value=3.5e-19  Score=163.32  Aligned_cols=98  Identities=18%  Similarity=0.177  Sum_probs=86.1

Q ss_pred             Cceeeec--ccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcCCCh---------------hHHHHHHHhcCCCH
Q psy938            5 GDGGLTT--PIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRTKDS---------------EVYDLLKLFSFDSL   66 (241)
Q Consensus         5 ~~~~lt~--pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~---------------~v~~~l~~~t~l~~   66 (241)
                      ++..+|.  |+|||+|| +|||||.+|+|||++   +|+++||||+++.|+               ++.+|+++||+  .
T Consensus       176 P~~~~~~~~p~l~gldG~~KMSKS~~n~I~L~d---~p~~i~~Ki~~a~td~~~~~~~~~~~p~~~~v~~~~~~~t~--~  250 (337)
T 2el7_A          176 PQALLNPEAPRVPGIDGKAKMSKSLGNTIGLLE---PEESIWQKIQHLPDDPQRIRLSDPGDPERTILFTYLSYFAP--K  250 (337)
T ss_dssp             CEEECCTTSCCCBCTTSSSBCCTTTTCCCBSSS---CHHHHHHHHHTCCCCC-------------CHHHHHHHHHSC--H
T ss_pred             CeeecccccccccCCCCccccCCCCCCeeeCcC---CHHHHHHHHHhCCCCCccccccCCCCCchhhHHHHHHHcCC--h
Confidence            4555766  99999999 999999999999999   899999999999665               79999999985  3


Q ss_pred             HHHHHHHHHhhc-CCChHHHHHHHHHHHHhhccCHHHHHHHH
Q psy938           67 AAIEDFKRQNEH-KPEERRAQKKLAEDLTLLVHGEEGLKSAK  107 (241)
Q Consensus        67 eei~~i~~~~~~-~~~~~~~Kk~LA~~i~~~vhG~~~a~~A~  107 (241)
                      ++++++++++.. +++++++|+.||++|++++||..+..+..
T Consensus       251 ~~i~~l~~~~~~g~~~~~~~K~~La~~i~~~l~p~re~~~~~  292 (337)
T 2el7_A          251 DLVEALKEEYRKAGVGTYVVKRILFDHLMEALRPIRERAEAL  292 (337)
T ss_dssp             HHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            699999999987 58999999999999999999987765443

>2dlc_X Tyrosyl-tRNA synthetase, cytoplasmic; tyrrs, ligase-tRNA complex; HET: 2MG OMG M2G PSU 6IA 5MC 5MU 1MA YMP; 2.40A {Saccharomyces cerevisiae}

Probab=99.76  E-value=6.4e-19  Score=164.55  Aligned_cols=112  Identities=12%  Similarity=0.095  Sum_probs=92.9

Q ss_pred             CCCceeeecccccCCC-CCccccCCCCe-EeecCCCCCHHHHHHHhhcC-------CChhHHHHHHH-------------
Q psy938            3 VTGDGGLTTPIIESES-GEKFGKSARNA-IWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKL-------------   60 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~d-G~KmsKS~gn~-I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~-------------   60 (241)
                      ...+++++.|+|+|+| |+|||||.+|+ |||++   +|+++++|++++       +|+++..|+++             
T Consensus       208 ~~~p~~l~~pll~gl~~G~KMSKS~~ns~I~L~D---~p~~i~kKI~ka~Td~~~~~d~~v~~y~k~~~~p~~~~~~~~g  284 (394)
T 2dlc_X          208 YKKRAHLMNPMVPGLAQGGKMSASDPNSKIDLLE---EPKQVKKKINSAFCSPGNVEENGLLSFVQYVIAPIQELKFGTN  284 (394)
T ss_dssp             CCCCEEEEECCCCCCC----------CCSCBTTC---CHHHHHHHHHHSCCCTTCCSSCHHHHHHHHTHHHHHHTSSSTT
T ss_pred             CCCCEEEecccccCCCCCCcCCCCCCCCEEeccC---CHHHHHHHHHHhcCCCCCCCcchHHHHHHhhhcchhhhcccCC
Confidence            3568999999999999 99999999996 99999   999999999986       68899999988             


Q ss_pred             ------------hcCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCC
Q psy938           61 ------------FSFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD  117 (241)
Q Consensus        61 ------------~t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~  117 (241)
                                  |++++.++++++++++..+ ++++++|+.||++|++++||..+..++...++.+|..+
T Consensus       285 ~~~~~i~~~~~~~~~~~~~~i~el~~~~~~g~~~~~~~K~~La~~i~~~l~p~r~~~~~~~~~~~~~~~~  354 (394)
T 2dlc_X          285 HFEFFIDRPEKFGGPITYKSFEEMKLAFKEEKLSPPDLKIGVADAINELLEPIRQEFANNKEFQEASEKG  354 (394)
T ss_dssp             CCCEEECCCGGGSCCEEESSHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred             CceEEEeccccccCcCCHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhHHHHHHHCCHHHHHHHhcc
Confidence                        7888888999999999877 89999999999999999999999888877788888754

>2g36_A Tryptophanyl-tRNA synthetase; TM0492, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI, ligase; HET: TRP; 2.50A {Thermotoga maritima}

Probab=99.75  E-value=3.6e-18  Score=156.74  Aligned_cols=91  Identities=20%  Similarity=0.114  Sum_probs=82.3

Q ss_pred             eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCCh---------------hHHHHHHHhcCCCHHHHHHH
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDS---------------EVYDLLKLFSFDSLAAIEDF   72 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~---------------~v~~~l~~~t~l~~eei~~i   72 (241)
                      ..++|+|||+||+|||||.+|+|||++   ||+++||||+++.++               ++.+|+++||+ +.++++++
T Consensus       192 ~~~~~~l~gldG~KMSKS~~n~I~L~d---sp~~i~~Ki~~a~td~~~~~~~~~~~p~~~~v~~~~~~f~~-~~~~ieel  267 (340)
T 2g36_A          192 LSRVPKLPGTDGRKMSKSYGNIINLEI---SEKELEQTILRMMTDPARVRRSDPGNPENCPVWKYHQAFDI-SEEESKWV  267 (340)
T ss_dssp             ECCSCCCCCTTSSCCCGGGTCCCBTTC---CHHHHHHHHHTCCCCTTCSSTTSCCCGGGCHHHHHHHHTTC-CHHHHHHH
T ss_pred             hccccccCCCCccccCCCCCCeEeeeC---CHHHHHHHHHhCCCCcccccccCCCCCchhHHHHHHHHHCC-CHhHHHHH
Confidence            445899999999999999999999999   999999999999654               89999999985 67888999


Q ss_pred             HHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           73 KRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        73 ~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      ++++..+ .+++++|+.||++|++++|+-..
T Consensus       268 ~~~~~~g~~~~~~~K~~La~~i~~~l~pire  298 (340)
T 2g36_A          268 WEGCTTASIGCVDCKKLLLKNMKRKLAPIWE  298 (340)
T ss_dssp             HHHHHTTCSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCChHHHHHHHHHHHHHHHHHHHH
Confidence            9999876 69999999999999999998554

>3tzl_A Tryptophanyl-tRNA synthetase; structural genomics, center for structural genomics of infec diseases, csgid, alpha-beta structure; HET: ADP TRP; 2.15A {Campylobacter jejuni subsp} SCOP: c.26.1.0 PDB: 3m5w_A*

Probab=99.73  E-value=3.1e-18  Score=156.14  Aligned_cols=93  Identities=16%  Similarity=0.163  Sum_probs=82.2

Q ss_pred             CceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCC-------------ChhHHHHHHHhcCCCHHHHHH
Q psy938            5 GDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTK-------------DSEVYDLLKLFSFDSLAAIED   71 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~-------------D~~v~~~l~~~t~l~~eei~~   71 (241)
                      +.+++|+|+|||+||+|||||.+|+|||++   ||+++++||+++.             ++.|.+|+++|+  +.+++++
T Consensus       176 ~~~~~~~~~l~~l~G~KMSKS~~n~I~L~d---~p~~i~~KI~~a~td~~~~~~~~~~~~~~v~~~~~~~~--~~~~i~~  250 (322)
T 3tzl_A          176 ARVNEEVAVVVGTDGAKMSKSYQNTIDIFS---SEKTLKKQISSIVTDSTALEDPKDHENCNIFKIAKLFL--DESGQKE  250 (322)
T ss_dssp             EECCCSSCCCBCTTSSBCCGGGTCCCBSSC---CHHHHHHHHHTCCCCCCCTTSCCCGGGCHHHHHHGGGC--CHHHHHH
T ss_pred             hhhccccccccCCCCCcCCCCCCCceecCC---CHHHHHHHHHhccCCCccccCCCCCcchhHHHHHHHhC--ChhHHHH
Confidence            345678999999999999999999999999   9999999999862             267888888886  7889999


Q ss_pred             HHHHhhc-CCChHHHHHHHHHHHHhhccCHHH
Q psy938           72 FKRQNEH-KPEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        72 i~~~~~~-~~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      +++++.. +++++++|+.||++|++.+|+-..
T Consensus       251 l~~~~~~g~~~~~~~K~~lae~l~~~l~pir~  282 (322)
T 3tzl_A          251 LQIRYEKGGEGYGHFKIYLNELVNAYFKEARE  282 (322)
T ss_dssp             HHHHHHHCSCCHHHHHHHHHHHHHHHTHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHhHHHHH
Confidence            9999876 489999999999999999998654

>1yi8_B Tryptophanyl-tRNA synthetase; ligase; HET: TRP; 2.10A {Deinococcus radiodurans} PDB: 1yia_B* 1yid_B* 2a4m_A*

Probab=99.71  E-value=2.1e-17  Score=152.29  Aligned_cols=95  Identities=22%  Similarity=0.264  Sum_probs=83.0

Q ss_pred             Cceeee-cccccCCCCC-ccccCCCCeEeecCCCCCHHHHHHHhhcC---------------CChhHHHHHHHhcCCCHH
Q psy938            5 GDGGLT-TPIIESESGE-KFGKSARNAIWLDSKLSSSFELYQYLIRT---------------KDSEVYDLLKLFSFDSLA   67 (241)
Q Consensus         5 ~~~~lt-~pLL~g~dG~-KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~---------------~D~~v~~~l~~~t~l~~e   67 (241)
                      ++..++ +|+|+|+||+ |||||.+|+|||++   +|+++||||+++               +++.+..|+++|++ +.+
T Consensus       197 P~~~~~~~~~l~~ldG~~KMSKS~~n~I~L~d---~p~~i~~Ki~~a~td~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~  272 (351)
T 1yi8_B          197 PQAQLSRVPRLPGLDGQAKMSKSLGNAIALGD---SADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDP-DPA  272 (351)
T ss_dssp             CEEEECSSCSCCCTTSSSCCCTTTTCCCBTTC---CHHHHHHHHHTCCCCTTCCSTTSCCCCTTCTTHHHHHHHCS-CHH
T ss_pred             CeeeeecCccccCCCCccccCCCCCCeecCCC---CHHHHHHHHHhcCCCcccccccCCCCCccchHHHHHHHHcC-Chh
Confidence            334464 8999999996 99999999999999   899999999975               34589999999986 788


Q ss_pred             HHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           68 AIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        68 ei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      +++++++++..+ .+++++|+.||++|++.+||-..-
T Consensus       273 ~ieel~~~~~~g~~~~~~~K~~La~~i~~~l~pire~  309 (351)
T 1yi8_B          273 RVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTR  309 (351)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHhhHHHHH
Confidence            889999999875 799999999999999999996653

>2cya_A Tyrosyl-tRNA synthetase; tyrrs, aminoacylation, structural genomics, NPPSFA, national on protein structural and functional analyses; 2.20A {Aeropyrum pernix}

Probab=99.71  E-value=1.4e-17  Score=154.02  Aligned_cols=98  Identities=19%  Similarity=0.267  Sum_probs=86.2

Q ss_pred             CCCceeeecccccCCC-----------------CCccccC-CCCeEeecCCCCCHHHHHHHhhcC-------CChhHHHH
Q psy938            3 VTGDGGLTTPIIESES-----------------GEKFGKS-ARNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDL   57 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~d-----------------G~KmsKS-~gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~   57 (241)
                      ..+++++++|+|+|++                 |+||||| .+|+|||++   +|+++||||+++       +|++|..|
T Consensus       203 ~~~p~~l~~~ll~~l~g~~~~~~~~~~~~~~~~g~KMSKS~~~~~I~L~d---~p~~i~~Ki~~a~td~~~~~~~~v~~~  279 (364)
T 2cya_A          203 RKKPVAIHTPIISSLQGPGRMEASQGEIDDVLAEVKMSKSKPETAVFVVD---SDDDIRRKIRKAYCPAKQVQGNPVLEI  279 (364)
T ss_dssp             CCCCEEEEECCCBCSSCC----------------CBCCSSSGGGSCBTTC---CHHHHHHHHHTSCCCTTCCTTCHHHHH
T ss_pred             CCCceeeccceeeCCCcccccccccccccccccccccCCCCCCCEeeccC---CHHHHHHHHHhCcCCCCCCCCCcHHHH
Confidence            3467899999999999                 6899999 689999999   999999999886       56899999


Q ss_pred             HHHhcC------------------CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           58 LKLFSF------------------DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        58 l~~~t~------------------l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      +++|+|                  ++.++++++++.+..+ ++++++|+.||++|++++|+-.+.
T Consensus       280 ~~~~~f~~~~~~~~i~r~~~~G~~~~~~~~~el~~~~~~g~~~~~~lK~~la~~l~~~l~pir~~  344 (364)
T 2cya_A          280 ARYILFARDGFTLRVDRPAKYGGPVEYTSYEELERDYTDGRLHPLDLKNAVAESLIEVVRPIRGA  344 (364)
T ss_dssp             HHHTTTTSTTCCEECC--------CEESSHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcccccCceeeeccccccCCCChHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999997                  3445899999999876 899999999999999999997654

>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}

Probab=99.70  E-value=9.8e-18  Score=139.02  Aligned_cols=84  Identities=12%  Similarity=0.187  Sum_probs=66.8

Q ss_pred             hcCCCceeeeccCC----CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecC--------CCC-----------cc
Q psy938          132 IFPGARIVELLMEP----GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQN--------PQE-----------VL  188 (241)
Q Consensus       132 ~~~~~p~~~~~~~~----~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d--------~~~-----------~l  188 (241)
                      .+..+|.+++....    +.+++++|+.+||++|++||||+|++|||||||+++.+        +..           .+
T Consensus        31 ~~~~~Pt~ei~lp~s~l~g~~ivdlLv~aGLa~SKsEARRlI~qGGv~VNg~kv~~~~~~~~i~~~~~~~tpi~d~~~~i  110 (164)
T 2ktl_A           31 NFANMPSARVTLPKSLVYDKTFSKVLWSAGLVASKSEGQRIINNNGAYVGSRPGVKKNEPGGGMPDDLTFTPIKTWNASK  110 (164)
T ss_dssp             TTTSTTCEEEECCGGGGGSCSHHHHHHHHTSCSTHHHHHHHHHHTCEEEEECCSCCCCCCCSSSCSSSCCCCCCCCSHHH
T ss_pred             ccccCCceeeccchhhhcCCcHHHHHHHhCcccCHHHHHHHHHhCCEEECCEeccccccccccccccccccccccccccc
Confidence            35667877664211    56899999999999999999999999999999988855        221           12


Q ss_pred             CCCCcccCCCeEEEEeccccEEEEEEcc
Q psy938          189 SPSAHILPNSLTLLRVEVSANIIAKSAN  216 (241)
Q Consensus       189 ~~~~~~~~~~~~llr~GKk~~~~i~~~~  216 (241)
                      . ..++++++|++||+|||+|++|++.+
T Consensus       111 t-~~dli~g~~liLRkGKK~~~lI~~~~  137 (164)
T 2ktl_A          111 T-QEFIIDGDLLILKLGKWKMKLVSIVS  137 (164)
T ss_dssp             H-HHHTTCSSCEEEEESSSCEEEEECCC
T ss_pred             C-HHHhcCCcEEEEEcCCeeEEEEEEec
Confidence            2 23578999999999999999999954

>2cyc_A Tyrosyl-tRNA synthetase; tyrosine, tyrrs, aminoacylation, structural genomics; HET: TYR; 2.20A {Pyrococcus horikoshii}

Probab=99.70  E-value=2.4e-17  Score=153.05  Aligned_cols=96  Identities=19%  Similarity=0.205  Sum_probs=87.2

Q ss_pred             CceeeecccccCCCC------------------CccccCC-CCeEeecCCCCCHHHHHHHhhc-------CCChhHHHHH
Q psy938            5 GDGGLTTPIIESESG------------------EKFGKSA-RNAIWLDSKLSSSFELYQYLIR-------TKDSEVYDLL   58 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG------------------~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~-------~~D~~v~~~l   58 (241)
                      +++++++|+|||++|                  +|||||. +|+|||++   +|+++||||++       ++|+++..|+
T Consensus       217 ~~~~~~~~~l~gL~g~~~~~~~~~~~~~~~~~~~KMSKS~~~~~I~L~d---~p~~i~~KI~~A~t~~~~~~~~~v~~~~  293 (375)
T 2cyc_A          217 KPVAVHHHLLLGLQEPPKWPIESEEEFKEIKAQMKMSKSKPYSAVFIHD---SPEEIRQKLRKAFCPAREVRYNPVLDWV  293 (375)
T ss_dssp             CCEEEEECCCBCSSCCSSSSCCSHHHHHHHHHHHBGGGSCGGGSCBTTC---CHHHHHHHHHHSCCCTTCCSSCHHHHHH
T ss_pred             ccEEeccccccCCCCcccccccchhhhhhhhhhhcccCCCCCCeeccCC---CHHHHHHHHHHhcCCCCCCCCChHHHHH
Confidence            678899999999999                  7999999 78999999   99999999988       4688999999


Q ss_pred             HHhcCCC------------------HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           59 KLFSFDS------------------LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        59 ~~~t~l~------------------~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      ++|+|.+                  .++++++++++..+ ++++++|+.||++|++++|+-.+.
T Consensus       294 ~~~~f~~~~~~~~i~~~~~~gg~~~~~~~~el~~~~~~g~~~~~~~K~~La~~l~~~l~pir~~  357 (375)
T 2cyc_A          294 EYIIFREEPTEFTVHRPAKFGGDVTYTTFEELKRDFAEGKLHPLDLKNAVAEYLINLLEPIRRY  357 (375)
T ss_dssp             HHTTTSSSSCCEEECCCGGGTCCEEESSHHHHHHHHHTTSSCHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             HHHhcCCCCcceeeecchhccCcCChhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999875                  56799999999877 899999999999999999997664

>1r6u_A Tryptophanyl-tRNA synthetase; class IC tRNA synthetase, rossmann fold catalytic domain, AN recognition domain, bound Trp-AMP, ligase; HET: TYM; 2.00A {Homo sapiens} SCOP: c.26.1.1 PDB: 1ulh_A 2dr2_A* 2ake_A* 1o5t_A

Probab=99.67  E-value=5.7e-17  Score=153.14  Aligned_cols=96  Identities=16%  Similarity=0.213  Sum_probs=85.9

Q ss_pred             CCceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C-CC-----------------hhHHHHHHHh
Q psy938            4 TGDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T-KD-----------------SEVYDLLKLF   61 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~-~D-----------------~~v~~~l~~~   61 (241)
                      ..+.++++|+|||+||  +|||||.+| +|||++   +|.++++|+++ + +|                 +.|.+|+++|
T Consensus       283 ~~P~~l~~pll~gLdG~~~KMSKS~~nsaI~L~D---~p~~I~kKI~~ya~td~~~~~~~~~~~g~~pd~~~v~~~l~~f  359 (437)
T 1r6u_A          283 PKPALLHSTFFPALQGAQTKMSASDPNSSIFLTD---TAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFF  359 (437)
T ss_dssp             CCCEEEEECCCEETTEEEEECCTTSSSSCCBTTC---CHHHHHHHHHHTSCCCBCSSHHHHHHHCBCTTTCHHHHHHHHH
T ss_pred             CCceEeecccccCCCCCccccCCCCCCCeeeccC---CHHHHHHHhhccccCCCccchhhccccCCCccHHHHHHHHHHH
Confidence            3456799999999999  799999999 899999   99999999999 4 22                 3689999999


Q ss_pred             cCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           62 SFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        62 t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      | ++.++|+++++++..+ ++++++|+.||++|++++||-...
T Consensus       360 t-~~~~eieel~~~~~~G~~~~~~~K~~LAe~i~~~l~~~rer  401 (437)
T 1r6u_A          360 L-EDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQAR  401 (437)
T ss_dssp             C-CCHHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             c-CCHhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            9 8999999999999887 899999999999999999987554

>2ip1_A Tryptophanyl-tRNA synthetase; rossmann fold, structural genomics, PSI-2, protein structure initiative; HET: PG4; 1.80A {Saccharomyces cerevisiae} PDB: 3kt0_A* 3kt3_A* 3kt6_A* 3kt8_A*

Probab=99.66  E-value=1.3e-16  Score=150.57  Aligned_cols=96  Identities=15%  Similarity=0.185  Sum_probs=80.0

Q ss_pred             CceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C-C-----------------ChhHHHHHHHhc
Q psy938            5 GDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T-K-----------------DSEVYDLLKLFS   62 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~-~-----------------D~~v~~~l~~~t   62 (241)
                      .++++++|+|||+||  +|||||.+| +|||++   +|.++++|+++ + .                 .+.|.+|+++|+
T Consensus       277 ~p~~l~~~ll~gLdG~~~KMSKS~~nsaI~L~d---~p~~i~~KI~~yA~t~~~~~~~~~~~~g~~pd~~~v~~~l~~f~  353 (432)
T 2ip1_A          277 KPALLHSRFFPALQGSTTKMSASDDTTAIFMTD---TPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFK  353 (432)
T ss_dssp             CCEEEEECCCCCTTC--------CGGGCCBTTC---CHHHHHHHHHHHSCCCSCSSHHHHHHHCCCTTTCHHHHHHHHHC
T ss_pred             CceeeccccccCCCCCccccCCCCCCCeEeccC---CHHHHHHHhhhhcccCCccchhhccccCCCchHHHHHHHHHHHC
Confidence            456799999999999  899999999 899999   99999999999 2 1                 146899999995


Q ss_pred             CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHHH
Q psy938           63 FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGLK  104 (241)
Q Consensus        63 ~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a~  104 (241)
                       ++.++++++++++..+ ++++++|+.||++|++++||-....
T Consensus       354 -~~~~eieel~~~~~~G~~~~~~~K~~La~~i~~~l~~~rer~  395 (432)
T 2ip1_A          354 -DDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERR  395 (432)
T ss_dssp             -CCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CCHhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence             8999999999999887 8999999999999999999977653

>2zp1_A Tyrosyl-tRNA synthetase; tRNA synthetases class I, ligase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, nucleotide-binding; HET: IYR; 1.70A {Methanocaldococcus jannaschii} PDB: 1zh6_A* 1j1u_A* 1u7d_A 2q1g_A* 2pxh_A* 1zh0_A* 2q1i_A* 2ag6_A* 3qe4_A* 3d6u_A* 3d6v_A* 1u7x_A 3n2y_A* 2hgz_A*

Probab=99.66  E-value=9.9e-17  Score=145.62  Aligned_cols=97  Identities=16%  Similarity=0.200  Sum_probs=83.9

Q ss_pred             CCceeeecccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhc-------------
Q psy938            4 TGDGGLTTPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFS-------------   62 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t-------------   62 (241)
                      .+++++++|+|||+|| +|||||.+|+|||++   +|+++++|++++       +++.+..|+++|.             
T Consensus       186 ~~~~~~~~~~l~~l~G~~KMSKS~~~~I~L~d---~~~~i~~KI~~a~td~~~~~~~~~~~~~~~~~~~~~~i~r~~k~g  262 (314)
T 2zp1_A          186 KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDD---SPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFG  262 (314)
T ss_dssp             SCCEEEEECCCBCTTSSSBCCTTTTCSCBTTC---CHHHHHHHHHHSCCCTTCCTTCHHHHHHHHHCCSSEEECCCGGGT
T ss_pred             CCcEEeeccccccCCcccccCCCCcceecCCC---CHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHhcCCcceeehhhcc
Confidence            4678899999999999 799999999999999   999999999998       2478899999985             


Q ss_pred             -CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           63 -FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        63 -~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                       .++.++++++++.+..+ ++++++|+.||++|++.+|+..+.
T Consensus       263 ~~~~~~~~eei~~~~~~g~~~~~~~K~~la~~i~~~l~p~r~~  305 (314)
T 2zp1_A          263 GDLTVNSYEELESLFKNKELHPMYLKNAVAEELIKILEPIRKR  305 (314)
T ss_dssp             CCEEESSHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence             23445677777777765 799999999999999999987654

>1r6t_A Tryptophanyl-tRNA synthetase; class IC tRNA synthetase, rossmann fold catalytical domain, recognition domain, bound Trp-AMP, ligase; HET: TYM; 2.10A {Homo sapiens} SCOP: a.16.1.3 c.26.1.1 PDB: 2azx_A* 2quh_A* 2qui_A* 2quj_A* 2quk_A

Probab=99.65  E-value=1.4e-16  Score=151.94  Aligned_cols=95  Identities=17%  Similarity=0.229  Sum_probs=84.8

Q ss_pred             CCceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C-----------------CC-hhHHHHHHHh
Q psy938            4 TGDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T-----------------KD-SEVYDLLKLF   61 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~-----------------~D-~~v~~~l~~~   61 (241)
                      ..++++++|+|||+||  +|||||.+| +|||++   +|.++++|+++ +                 +| +.|.+|+++|
T Consensus       330 ~~p~~l~~pll~gLdG~~~KMSKS~~nsaI~L~d---~p~~i~kKi~~yA~t~~~~~~~~~~~~g~~pd~~~v~~~l~~f  406 (477)
T 1r6t_A          330 PKPALLHSTFFPALQGAQTKMSASDPNSSIFLTD---TAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTFF  406 (477)
T ss_dssp             CCCEEEEECCCEETTEEEEECCTTSTTCCCBTTC---CHHHHHHHHHHHSCCCSCSSHHHHHHHCCCTTTCHHHHHHHHH
T ss_pred             CCceeeecccccCCCCCccccCCCCCCCceeecC---CHHHHHHHhccccccCCccchhhccccCCCchHHHHHHHHHHH
Confidence            3466799999999999  799999999 899999   99999999999 2                 12 4689999999


Q ss_pred             cCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           62 SFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        62 t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      | ++.++|+++++++..+ ++++++|+.||++|++++|+-..
T Consensus       407 t-~~~~eieel~~~~~~G~~~~~~~K~~Lae~i~~~l~pire  447 (477)
T 1r6t_A          407 L-EDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQA  447 (477)
T ss_dssp             C-CCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             c-CCHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9 8999999999999887 89999999999999999997543

>2cyb_A Tyrosyl-tRNA synthetase; rossmann-fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: TYR; 1.80A {Archaeoglobus fulgidus}

Probab=99.63  E-value=3.6e-16  Score=142.26  Aligned_cols=96  Identities=18%  Similarity=0.213  Sum_probs=84.8

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhc-------------
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFS-------------   62 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t-------------   62 (241)
                      ..++++++.|+|+++||+|||||.||+|||++   +|.++++|++++       +++.+..|+++|.             
T Consensus       196 ~~~p~~l~~pll~~l~G~KMSKS~~n~I~l~d---~p~~i~~Ki~~a~td~~~~~~~~~~~~~~~~~~p~~~~~~i~~~~  272 (323)
T 2cyb_A          196 YSSPVCLHTPILVGLDGQKMSSSKGNYISVRD---PPEEVERKIRKAYCPAGVVEENPILDIAKYHILPRFGKIVVERDA  272 (323)
T ss_dssp             CCCCEEEEECCCBCTTSSBCCTTTTCSCBTTC---CHHHHHHHHHTSCCCTTCCTTCHHHHHHHHTHHHHHSCEEECCCG
T ss_pred             CCCceEEecCcccCCCCCcccCCcCceeCCCC---CHHHHHHHHHhcCCCCCCCCcChHHHHHHHHhccccCceeEechh
Confidence            34688999999999999999999999999999   999999999998       4688999999985             


Q ss_pred             ----CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938           63 ----FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        63 ----~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                          .++.++++++++++..| .+++++|+.||+.|++.++.-.
T Consensus       273 ~~G~~~~~~~~~~l~~~~~~g~~~~~~~K~~la~~i~~~l~pir  316 (323)
T 2cyb_A          273 KFGGDVEYASFEELAEDFKSGQLHPLDLKIAVAKYLNMLLEDAR  316 (323)
T ss_dssp             GGTCCEEESSHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcCCCCCcccHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence                33556888899998876 7999999999999999987643

>3hzr_A Tryptophanyl-tRNA synthetase; APO tRNA-ligase, structural genomics, medical structural GEN pathogenic protozoa, MSGPP, ligase; 3.00A {Entamoeba histolytica}

Probab=99.59  E-value=1.9e-15  Score=140.71  Aligned_cols=95  Identities=16%  Similarity=0.223  Sum_probs=83.6

Q ss_pred             CCceeeecccccCCCC-CccccC-CCCeEeecCCCCCHHHHHHHhhcC-------CC------------hhHHHHHHHhc
Q psy938            4 TGDGGLTTPIIESESG-EKFGKS-ARNAIWLDSKLSSSFELYQYLIRT-------KD------------SEVYDLLKLFS   62 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG-~KmsKS-~gn~I~L~~~~Tsp~~~yq~~~~~-------~D------------~~v~~~l~~~t   62 (241)
                      .+++.+++|+|+|+|| +||||| .+|+|||++   +|+++++|++++       +|            +.+.+|+++|+
T Consensus       251 ~~p~~l~~~~l~gLdG~~KMSKSd~~~~I~L~D---~p~~i~kKI~k~A~t~g~~Td~~~~~~~g~p~~~~v~~~~~~~~  327 (386)
T 3hzr_A          251 IQPTVLFHKMVPLLSGVTKFDIPSDHNSILLSD---NAKQVERKINKLAFSGGRNTTEEHKKLGGQCDIDVSFQLLNIFS  327 (386)
T ss_dssp             CCCEEEEECCCCCTTCTTCCCCCCTTTSCBTTC---CHHHHHHHHHHTSCCCCCSSHHHHHTTCCCGGGCHHHHHHHHHC
T ss_pred             CCceEeecCeeeCCCCCCccCcCCCCCeeecCC---CHHHHHHHHHHhccCCCCCCcccccccCCCCccchHHHHHHHHc
Confidence            4568889999999999 599999 799999999   999999999995       22            56889999998


Q ss_pred             CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           63 FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        63 ~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                       .+.++++++.+++..+ .+++++|+.||++|++.+++-..
T Consensus       328 -~~~~~~eei~~~~~~G~l~~g~~K~~lae~i~~~l~pire  367 (386)
T 3hzr_A          328 -SDNAQVKDVEEKYSKGELLSGELKKIVSASMKDFIVAYDA  367 (386)
T ss_dssp             -SCHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             -CChhhHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence             6888999999999765 69999999999999999987554

>1i6k_A TRPRS, tryptophanyl-tRNA synthetase; class I tRNA synthetase, AARS, induced FIT, ligase; HET: TYM; 1.72A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 1i6l_A* 1i6m_A* 1m83_A* 1mau_A* 1maw_A* 1mb2_A* 2ov4_A* 3fhj_A* 3fi0_A* 1d2r_A 3u1v_A

Probab=99.58  E-value=1e-15  Score=139.82  Aligned_cols=87  Identities=22%  Similarity=0.164  Sum_probs=79.1

Q ss_pred             cccccCCCC--CccccCCCC-e--EeecCCCCCHHHHHHHhhcC-C------------ChhHHHHHHHhcCCCHHHHHHH
Q psy938           11 TPIIESESG--EKFGKSARN-A--IWLDSKLSSSFELYQYLIRT-K------------DSEVYDLLKLFSFDSLAAIEDF   72 (241)
Q Consensus        11 ~pLL~g~dG--~KmsKS~gn-~--I~L~~~~Tsp~~~yq~~~~~-~------------D~~v~~~l~~~t~l~~eei~~i   72 (241)
                      +|+|+|+||  +|||||.+| +  |||++   +|+++++|++++ +            |++|.+++.+|++++.++++++
T Consensus       180 ~~~l~gl~G~~~KMSKS~~n~~~~I~L~d---~~~~i~~KI~~a~td~~~~~~~~~~~~p~v~~~~~~~~~~~~~~~~el  256 (328)
T 1i6k_A          180 GARIMSLVDPTKKMSKSDPNPKAYITLLD---DAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEEL  256 (328)
T ss_dssp             SSSCBCSSCTTSBCCTTCSCGGGCCBTTC---CHHHHHHHHHHCCCCSSCCCCCBTTTBHHHHHHHHHHHHHHCCCHHHH
T ss_pred             cccccCCCCCccCCCCCCCCcCceeeecC---CHHHHHHHHHhcCCCCccccccCCCCCcchhhHHHHHHHCCchhHHHH
Confidence            789999999  899999999 7  99999   999999999997 1            4778899999998888899999


Q ss_pred             HHHhhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           73 KRQNEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        73 ~~~~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      ++++. +++++++|+.||++|++++|.-.
T Consensus       257 ~~~~~-g~~~~~~K~~La~~i~~~l~pir  284 (328)
T 1i6k_A          257 ERQYE-GKGYGVFKADLAQVVIETLRPIQ  284 (328)
T ss_dssp             HHHTT-TCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHc-CCCHHHHHHHHHHHHHHHhHHHH
Confidence            99998 89999999999999999998644

>3jxe_A Tryptophanyl-tRNA synthetase; adenosine triphosphate, rossmann fold, crystallography, X-RAY, P. horikoshii, aminoacyl-tRNA synthetase; HET: TYM; 3.00A {Pyrococcus horikoshii}

Probab=99.56  E-value=6.5e-15  Score=137.41  Aligned_cols=96  Identities=13%  Similarity=0.167  Sum_probs=83.1

Q ss_pred             CCceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc--CCCh-----------------hHHHHHHHh
Q psy938            4 TGDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR--TKDS-----------------EVYDLLKLF   61 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~--~~D~-----------------~v~~~l~~~   61 (241)
                      ..+.++++|+|+|+||  +|||||.+| +|||++   +|.++++|+++  .+|+                 .+.+|+.+|
T Consensus       234 ~~p~~l~~~~l~gLdG~~~KMSKS~~ns~I~L~D---~p~~I~kKI~k~A~td~~~~~~~~~~~~~~P~~~~~~~~l~~~  310 (392)
T 3jxe_A          234 YKTAALHSKFVPSLTSLSGKMSASKPETAIYLTD---SPEDVEKKVWKFTLTGGRPTLKEQREKGGEPEKCVVFKWLEIF  310 (392)
T ss_dssp             CCCEEEEECCCCCSSCSSSCCCTTSGGGCCBTTC---CHHHHHHHHHTCC--------------------CHHHHHHHHT
T ss_pred             CCCeeeecccccCCCCCccccccCCCCCeeeCCC---CHHHHHHHHHhhccCCCCcccccccccCCCCchhHHHHHHHHH
Confidence            4678899999999999  599999998 999999   99999999999  4554                 256899999


Q ss_pred             cCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           62 SFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        62 t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      +..+.++++++.+++..| .+++++|+.||+.|++.++.-..
T Consensus       311 ~~~~~~~~eel~~~~~~G~l~~gdlK~~lae~i~~~l~pire  352 (392)
T 3jxe_A          311 FEEDDKKLKERYYACKNGELTCGECKRYLISKIQEFLKEHQR  352 (392)
T ss_dssp             TCCCHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCcchHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            888899999999999876 69999999999999999987554

>3hv0_A Tryptophanyl-tRNA synthetase; tRNA-ligase, ATP-binding, aminoacyl-tRNA synthetase, ligase, nucleotide-binding; HET: TRP; 2.42A {Cryptosporidium parvum iowa II} SCOP: c.26.1.0

Probab=99.56  E-value=5.1e-15  Score=138.22  Aligned_cols=97  Identities=11%  Similarity=0.231  Sum_probs=73.5

Q ss_pred             CCCceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhc-C-CC-----------------hhHHHHHHH
Q psy938            3 VTGDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIR-T-KD-----------------SEVYDLLKL   60 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~-~-~D-----------------~~v~~~l~~   60 (241)
                      ..+++++++|+|||+||  +|||||.+| +|||++   +|.++++|+++ + +|                 +.+..|+.+
T Consensus       246 ~~~p~~l~~~~l~gLdG~~~KMSKS~~nsaI~L~D---~p~~i~kKI~k~A~td~~~~~~~~~~~~g~p~~~~~~~~~~~  322 (393)
T 3hv0_A          246 YLKPSSIHSIFLPSLQGSQTKMSASVQNSSIFVND---NEESIRNKIMKYAFSGGQATEEEQRRLGANLDVDVSWQYLRF  322 (393)
T ss_dssp             CCCCEEEEECCCCC-------------CCCCBTTC---CHHHHHHHHHHHSCCCSCSSSCCC---CCCTTTCHHHHHHHH
T ss_pred             CCCceeeccCcccCCCCCCcCCCCCCCCCeEeccC---CHHHHHHHHHhhccCCCCccccccccCCCCcchhHHHHHHHH
Confidence            45788999999999999  799999987 999999   99999999999 4 22                 357788888


Q ss_pred             hcCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           61 FSFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        61 ~t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      |+ .+.++++++.+++..| .+++++|+.||+.|++.+++-...
T Consensus       323 ~~-~~~~~~eei~~~y~~G~l~~g~~K~~lae~i~~~l~pirer  365 (393)
T 3hv0_A          323 LM-EDDEKLEEIGKKYSSGEMLSGEIKSILVQELVKLTKNHQKN  365 (393)
T ss_dssp             HC-CCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             Hc-CChhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            86 4788999999999866 699999999999999999986654

>3i05_A Tryptophanyl-tRNA synthetase; APO tRNA-ligase, ATP-binding, aminoacyl-tRNA synthetase, LIG nucleotide-binding, protein biosynthesis; 2.80A {Trypanosoma brucei} SCOP: c.26.1.0

Probab=99.55  E-value=3.1e-15  Score=139.75  Aligned_cols=95  Identities=13%  Similarity=0.138  Sum_probs=64.4

Q ss_pred             CCCceeeecccccCCCC--CccccCCCCeEeecCCCCCHHHHHHHhhcC--CC-----------------hhHHHHHHHh
Q psy938            3 VTGDGGLTTPIIESESG--EKFGKSARNAIWLDSKLSSSFELYQYLIRT--KD-----------------SEVYDLLKLF   61 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG--~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~--~D-----------------~~v~~~l~~~   61 (241)
                      ..+++++++|+|||+||  +|||||.+|+|||++   +|+++++|++++  +|                 +.+..|+.+|
T Consensus       250 ~~~p~~l~~~~l~gLdG~~~KMSKS~~~~I~L~D---~p~~i~kKI~k~A~td~~~~~e~~~~~~g~p~v~~~~~~~~~~  326 (395)
T 3i05_A          250 YLKPAVIHSKFFPGLSGPKGKMSSSSGTAVLLTD---TEKMVKDKINKHAFSGGGATKQEHFLLGANVEVDVPIQWLSFF  326 (395)
T ss_dssp             CCCCEEEEECCCCCC-------------CCBTTC---CHHHHHHHHC----------------------CCHHHHHHHHH
T ss_pred             CCCceeeccccccCCCCCcccCCCCCCCcccCCC---CHHHHHHHHHhhccCCCccchhhcccCCCCcchhHHHHHHHHH
Confidence            45788999999999999  799999999999999   999999999993  32                 2467888888


Q ss_pred             cCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHH
Q psy938           62 SFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        62 t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      + .+.++++++.+++..| .+++++|+.||+.|++.+..-.
T Consensus       327 ~-~~~~~~eei~~~y~~G~l~~g~lK~~lae~i~~~l~pir  366 (395)
T 3i05_A          327 L-EDDEELARVKKEYMLGRIMTGEVKKLLINTITAITKTHQ  366 (395)
T ss_dssp             C-CCSHHHHHHCC-------CHHHHHHHHHHHHHHHHHHHH
T ss_pred             c-CChhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6 4678899999888866 6999999999999999876543

>3tze_A Tryptophanyl-tRNA synthetase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, amino acylation; HET: TRP; 2.60A {Encephalitozoon cuniculi}

Probab=99.54  E-value=9.8e-15  Score=136.76  Aligned_cols=97  Identities=13%  Similarity=0.186  Sum_probs=83.7

Q ss_pred             CCCceeeecccccCCCC--CccccCC-CCeEeecCCCCCHHHHHHHhhc--CCC-----------------hhHHHHHHH
Q psy938            3 VTGDGGLTTPIIESESG--EKFGKSA-RNAIWLDSKLSSSFELYQYLIR--TKD-----------------SEVYDLLKL   60 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG--~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~--~~D-----------------~~v~~~l~~   60 (241)
                      ..+++++++|+|||+||  +|||||. +|+|||++   +|.++++|+++  .+|                 +.+..|+++
T Consensus       269 ~~~p~~l~~~~l~gLdG~~~KMSKS~~~~~I~L~D---~p~~I~kKI~k~A~td~~~~~e~~~~~~g~p~v~~l~~~~~~  345 (406)
T 3tze_A          269 EKKPSSIYVSLLPDLKGVNRKMSASDPNSSIYLDD---AQDTIRKKIIAYAYSGGRKTLEEHREKGGDIDVDVPFEYLKY  345 (406)
T ss_dssp             CCCCEEEEECCCCCTTSCCCCSSCSCGGGSCBTTC---CHHHHHHHHHHHCCCCCCCC-------CCCGGGCHHHHHHHH
T ss_pred             CCCceeeccCcccCCCCCCcCCCCCCCCCcccCCC---CHHHHHHHHHhhccCCCcccccccccCCCCCcccHHHHHHHH
Confidence            35678999999999999  6999999 78999999   99999999999  454                 247888888


Q ss_pred             hcCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHHH
Q psy938           61 FSFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEGL  103 (241)
Q Consensus        61 ~t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~a  103 (241)
                      |+. +.++++++.+++..+ .+++++|+.||+.|++.++.-...
T Consensus       346 ~~~-~~~~~eei~~~y~~G~l~~g~lK~~Lae~i~~~l~pirer  388 (406)
T 3tze_A          346 FLD-DDQELEKYRSGYIKGEITSKEMKEKCVVVIQEFVSRYQES  388 (406)
T ss_dssp             HCC-CHHHHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HcC-CcchHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            873 678999999998766 699999999999999999875543

>2j5b_A Tyrosyl-tRNA synthetase; ligase, protein biosynthesis, ATP-binding; HET: TYE; 2.20A {Acanthamoeba polyphaga mimivirus}

Probab=99.54  E-value=4.4e-15  Score=136.55  Aligned_cols=94  Identities=16%  Similarity=0.245  Sum_probs=80.4

Q ss_pred             CCceeeecccccCC-CC-CccccCC-CCeEeecCCCCCHHHHHHHhhcCCC------hhHHHHHHHhcC----------C
Q psy938            4 TGDGGLTTPIIESE-SG-EKFGKSA-RNAIWLDSKLSSSFELYQYLIRTKD------SEVYDLLKLFSF----------D   64 (241)
Q Consensus         4 ~~~~~lt~pLL~g~-dG-~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~~D------~~v~~~l~~~t~----------l   64 (241)
                      ..++.++.|+|||+ || +|||||. +|+|||++   +|.++++|++++.+      +.+..|++++++          +
T Consensus       213 ~~p~~~~~~~l~gL~dg~~KMSKS~~~~~I~L~d---~p~~i~kKI~ka~td~~~~~~~~~~~~~~~~~~~~~~~~i~~~  289 (348)
T 2j5b_A          213 KIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDD---TEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGK  289 (348)
T ss_dssp             CCCEEEEBCCCCCTTCSSCCCSTTCGGGSCBTTC---CHHHHHHHHHHSCCCSSSTTCHHHHHHHHTHHHHHSCEEETTE
T ss_pred             CCceeecCccccCCCCcccccccCCCCCeEeecC---CHHHHHHHHhcccCCCCCCCCchHhHHHHhhhhhhcccccccC
Confidence            34667899999999 67 6999999 68999999   99999999999844      578999888643          3


Q ss_pred             CHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           65 SLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        65 ~~eei~~i~~~~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      +.++++++++++. +.+++++|+.||++|++.+|.-.
T Consensus       290 ~~~~~~el~~~~~-~~~~~~~K~~la~~l~~~l~pir  325 (348)
T 2j5b_A          290 IYTDIESIQEDFS-SMNKRELKTDVANYINTIIDLVR  325 (348)
T ss_dssp             EESSHHHHHHHHT-TSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHc-ccCHHHHHHHHHHHHHHHHHHHH
Confidence            4567888998888 88999999999999999998643

>2yy5_A Tryptophanyl-tRNA synthetase; aminoaccyl tRNA synthetase, structural genomics, NPPSFA; HET: WSA; 2.55A {Mycoplasma pneumoniae}

Probab=99.53  E-value=4.4e-15  Score=136.62  Aligned_cols=93  Identities=16%  Similarity=0.126  Sum_probs=81.6

Q ss_pred             Cceeee--cccccCCCC--CccccCCCC---eEeecCCCCCHHHHHHHhhcCC-------------ChhHHHHHHHhcCC
Q psy938            5 GDGGLT--TPIIESESG--EKFGKSARN---AIWLDSKLSSSFELYQYLIRTK-------------DSEVYDLLKLFSFD   64 (241)
Q Consensus         5 ~~~~lt--~pLL~g~dG--~KmsKS~gn---~I~L~~~~Tsp~~~yq~~~~~~-------------D~~v~~~l~~~t~l   64 (241)
                      ++..++  +|+|+|+||  +|||||.+|   +|||++   +|+++++|++++.             |+++.+++.+|+++
T Consensus       182 P~~l~~~~~~~l~gL~g~~~KMSKS~~n~~~~I~L~D---~~~~i~~KI~~a~td~~~~~~~~~~~~p~v~~~~~~~~~~  258 (348)
T 2yy5_A          182 PQFVQNKDTNRIMDLFDPTKKMSKSSKNQNGVIYLDD---PKEVVVKKIRQATTDSFNKIRFASKTQPGVTNMLTILKAL  258 (348)
T ss_dssp             CEEECCTTTTTCBCSSCTTSBCCSSCSCGGGCCBTTC---CHHHHHHHHHTCCCCSSCCCSCCTTTCHHHHHHHHHHHHH
T ss_pred             CeeecccccccccCCCCcchhcCCCCCCCCceEeecC---CHHHHHHHHHhCCCCCccccccCCCCCCchhhHHHHHHhC
Confidence            344454  799999999  899999999   899999   9999999999972             36788999999988


Q ss_pred             CHHHHH---------HHHHHhhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           65 SLAAIE---------DFKRQNEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        65 ~~eei~---------~i~~~~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      +.++++         ++++++. +.+++++|+.||++|++.++.-.
T Consensus       259 ~~~~~~~~~~~~~~~el~~~~~-g~~~~~~K~~La~~i~~~l~pir  303 (348)
T 2yy5_A          259 LKEPVNQSLTNQLGNDLEAYFS-TKSYLDLKNALTEATVNLLVNIQ  303 (348)
T ss_dssp             TTSGGGHHHHHHHCSCHHHHGG-GCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ChHhhhhhcccchHHHHHHHHc-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            889999         9999998 79999999999999999987643

>3vgj_A Tyrosyl-tRNA synthetase, putative; tyrrs, ligase; HET: YAP; 2.21A {Plasmodium falciparum}

Probab=99.48  E-value=4.1e-14  Score=131.25  Aligned_cols=95  Identities=15%  Similarity=0.220  Sum_probs=78.0

Q ss_pred             CceeeecccccCC-CC-CccccCC-CCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhc-----C------
Q psy938            5 GDGGLTTPIIESE-SG-EKFGKSA-RNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFS-----F------   63 (241)
Q Consensus         5 ~~~~lt~pLL~g~-dG-~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t-----~------   63 (241)
                      +++++++|+|+|+ || +|||||. +|+|||++   +|+++++|++++       +++.+..|++++.     .      
T Consensus       229 ~~~~l~~p~l~gL~dG~~KMSKS~~~~~I~L~D---~p~~i~~KI~kA~td~~~~~~n~~~~~~~~~~f~~~~~f~~~~~  305 (373)
T 3vgj_A          229 KPVILSHGMLPGLLEGQEKMSKSDENSAIFMDD---SESDVNRKIKKAYCPPNVIENNPIYAYAKSIIFPSYNEFNLVRK  305 (373)
T ss_dssp             CCEEEEBCCCCCSSTTCCSCCSSSTTCCCBTTC---CHHHHHHHHHHSCCCTTCCTTCHHHHHHHHTHHHHHSSEEECCC
T ss_pred             CceEEeCCeeecCCCCCCCCcCCCCCCeeecCC---CHHHHHHHHHhCcCCCCCCCCCcchhhhhhhhhhhhhhhccccc
Confidence            4688999999997 99 5999999 58999999   999999999997       5667777765432     1      


Q ss_pred             ------CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           64 ------DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        64 ------l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                            ++.++++++++++..+ .+|+++|+.||+.|++.+..-..
T Consensus       306 ~~~g~~~~~~~~eel~~~~~~g~l~~~dlK~~lae~i~~~l~Pire  351 (373)
T 3vgj_A          306 EKNGGDKTYYTLQELEHDYVNGFIHPLDLKDNVAMYINKLLQPVRD  351 (373)
T ss_dssp             GGGTCCEEECCHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCCcCcccHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence                  1235788899888866 69999999999999999886443

>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, tyrrs, pseudod translation, ATP-binding, nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania major} PDB: 3p0i_A* 3p0h_A*

Probab=99.47  E-value=6.4e-14  Score=138.83  Aligned_cols=92  Identities=16%  Similarity=0.263  Sum_probs=79.9

Q ss_pred             CceeeecccccCC-CC-CccccCCC-CeEeecCCCCCHHHHHHHhhcC----------------------CChhHHHHHH
Q psy938            5 GDGGLTTPIIESE-SG-EKFGKSAR-NAIWLDSKLSSSFELYQYLIRT----------------------KDSEVYDLLK   59 (241)
Q Consensus         5 ~~~~lt~pLL~g~-dG-~KmsKS~g-n~I~L~~~~Tsp~~~yq~~~~~----------------------~D~~v~~~l~   59 (241)
                      +++++++|+|+|+ || +|||||.+ |+|||++   +|+++++|++++                      +++.+..|++
T Consensus       212 ~p~~l~~~~l~gL~dG~~KMSKS~~~~~I~L~D---~p~~i~kKI~~A~td~~~~~~~~~~d~g~~~~~~~~~~v~~y~~  288 (690)
T 3p0j_A          212 KPVILSHHMLAGLKQGQAKMSKSDPDSAIFMED---TEEDVARKIRQAYCPRVKQSASAITDDGAPVATDDRNPVLDYFQ  288 (690)
T ss_dssp             CCEEEEBCCCCCSSTTCSSCBTTBGGGSCBTTC---CHHHHHHHHHTSCCCSSCCCCCCCCTTCCCCCCSSCCHHHHHHH
T ss_pred             CceEeecCeeecCCCCCcCCCCCCCCCeeeccC---CHHHHHHHHHhCcCCCcccccccccCCCCcccCCCCchHHHHHH
Confidence            4688999999999 99 59999997 7999999   999999999997                      4678999999


Q ss_pred             HhcCC-----------CHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           60 LFSFD-----------SLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        60 ~~t~l-----------~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      +|.+.           +.++++++.+++..+ .+|+++|+.||+.|++.+..
T Consensus       289 ~~~~~~~~~~~~~~~~~~~~~eel~~~y~~G~l~~~dlK~~lae~i~~~L~P  340 (690)
T 3p0j_A          289 CVVYARPGAAATIDGTTYATYEDLEQAFVSDEVSEDALKSCLIDEVNALLEP  340 (690)
T ss_dssp             HTTTTSTTCCEEETTEEESSHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcccccccccccCCCcchHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            98653           346788999998876 69999999999999996654

>3foc_A Tryptophanyl-tRNA synthetase; structural genomics, giardiasi aminoacyl-tRNA synthetase, ligase; 2.09A {Giardia lamblia atcc 50803}

Probab=99.38  E-value=6.9e-13  Score=125.57  Aligned_cols=95  Identities=18%  Similarity=0.191  Sum_probs=81.3

Q ss_pred             CCceeeecccccCCCCC--ccccCCCC-eEeecCCCCCHHHHHHHhhcC--CC-----------------hhHHHHHHHh
Q psy938            4 TGDGGLTTPIIESESGE--KFGKSARN-AIWLDSKLSSSFELYQYLIRT--KD-----------------SEVYDLLKLF   61 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~--KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~--~D-----------------~~v~~~l~~~   61 (241)
                      .++..+++|+|+|+||.  |||||.+| +|+|.+   +|.++++|+|++  +|                 +.+++|+.+|
T Consensus       314 ~~p~~~~~~~l~gLdG~~~KMSKS~~ns~I~l~D---~p~~I~kKI~k~A~Td~~~~~~~~~~~~g~p~~~~v~~~l~~f  390 (451)
T 3foc_A          314 PKNAYLLGKFLPGLQGSGTKMSASDPNSAIYLTD---TPAQIKNKINRYAFSGGRDTEEEHRAFGADLSVDVSVRYLEVF  390 (451)
T ss_dssp             CCCEEEEECCCCBTTBTTCCCCTTCGGGSCBTTC---CHHHHHHHHHHHSCCCSCSSHHHHHTTCCCTTTCHHHHHHHHH
T ss_pred             CCCeeecCCcccCCCCCCCccCCCCCCCeeeecC---CHHHHHHHHhhhccCCCCccchhcccCCCCcchhhHHHHHHHH
Confidence            45677899999999994  99999987 899999   999999999993  43                 1367888888


Q ss_pred             cCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           62 SFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        62 t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      + .+.++++++.+++..+ .+++++|+.||+.|++.+..-..
T Consensus       391 ~-~~~~~~eel~~~y~~G~l~~g~lK~~Lae~i~~~l~pire  431 (451)
T 3foc_A          391 M-KDDAELEKLKADYKTGKLLTGEVKATLIGILQGLIKEHAE  431 (451)
T ss_dssp             C-CCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             c-CCHhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            7 6788999999999875 69999999999999999876443

>3a04_A Tryptophanyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, nucleotide-binding, protein biosynthesis; 1.97A {Aeropyrum pernix} PDB: 3a05_A*

Probab=99.22  E-value=5e-11  Score=110.51  Aligned_cols=92  Identities=13%  Similarity=0.092  Sum_probs=75.7

Q ss_pred             CceeeecccccCCCCCccccCC-CCeEeecCCCCCHHHHHHHhhcC-CC--------------hh---HHHHHHHhcCCC
Q psy938            5 GDGGLTTPIIESESGEKFGKSA-RNAIWLDSKLSSSFELYQYLIRT-KD--------------SE---VYDLLKLFSFDS   65 (241)
Q Consensus         5 ~~~~lt~pLL~g~dG~KmsKS~-gn~I~L~~~~Tsp~~~yq~~~~~-~D--------------~~---v~~~l~~~t~l~   65 (241)
                      .+..+.+|+++|+||.|||||. +|+|+|.+   +|.++++|++++ +|              ++   +..|..++.+-+
T Consensus       240 ~P~~~~~~~~pgldG~KmS~S~~ns~I~l~D---~p~~i~kKI~ka~td~~~~~~~~~~~~G~p~~~~i~~~~l~~~~~d  316 (372)
T 3a04_A          240 RPASTYHKLQPGLDGRKMSSSRPDSTIFLTD---PPEVARNKLFRALTGGRATAEEQRRLGGVPEVCSVYHMDLYHLMPD  316 (372)
T ss_dssp             CCEEEEECCCBCTTSSBCCTTSGGGSCBTTC---CHHHHHHHHHTCCCSCCSSHHHHHHHCCCGGGCHHHHHHHHTTCCS
T ss_pred             ChhhhhhcccCCCCCCccCCCCCCcccccCC---CHHHHHHHHhcCccCCCCCcccccccCCCCchhhHHHHHHHccCCC
Confidence            4567788999999999999998 55899999   999999999997 22              23   344444455457


Q ss_pred             HHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           66 LAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        66 ~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                      .++++++.++++.| .++.++|+.||+.|++.+..
T Consensus       317 ~~e~~ei~~~y~~G~l~~ge~K~~l~e~l~~~l~p  351 (372)
T 3a04_A          317 DGEVKHIYTSCRLGKILCGECKQIAWEKLERFLAE  351 (372)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence            88999999999876 79999999999999999865

>3sz3_A Tryptophanyl-tRNA synthetase; structural genomics, center for structural genomics of infec diseases, csgid, rossmann fold; HET: TRP; 1.50A {Vibrio cholerae o1 biovar el tor}

Probab=99.18  E-value=6.5e-12  Score=115.22  Aligned_cols=85  Identities=14%  Similarity=0.142  Sum_probs=66.8

Q ss_pred             cccccCC-CC-CccccCC---CCeEeecCCCCCHHHHHHHhhcC-CCh-----------------hHHHHHHHhcCCCHH
Q psy938           11 TPIIESE-SG-EKFGKSA---RNAIWLDSKLSSSFELYQYLIRT-KDS-----------------EVYDLLKLFSFDSLA   67 (241)
Q Consensus        11 ~pLL~g~-dG-~KmsKS~---gn~I~L~~~~Tsp~~~yq~~~~~-~D~-----------------~v~~~l~~~t~l~~e   67 (241)
                      .|+|+|+ || +|||||.   +|+|||++   +|+++++|++++ +|+                 .+..|+..|++   +
T Consensus       189 ~~~l~gL~dg~~KMSKS~~~~~~~I~L~D---~p~~i~kKI~~a~Td~~~~~~~~~~~~~~p~v~~l~~~~~~~~~---~  262 (341)
T 3sz3_A          189 NARVMSLQDATKKMSKSDDNRKNVITLLE---DPKSIIKKINKAQTDAETPPRIAYDVENKAGIANLMGLYSAATG---K  262 (341)
T ss_dssp             CCCCEETTEEEEECCTTCSCGGGCCBTTC---CHHHHHHHHHTCCCCCCSSCCCCCCTTTCHHHHHHHHHHHHHHC---C
T ss_pred             cccccCCCCCCCccCCCCCCCCCeeecCC---CHHHHHHHhhhccCCCCCCcccccCCCCCcchhHHHHHHHHcCC---c
Confidence            3556678 68 6999999   78999999   999999999998 332                 34555555554   5


Q ss_pred             HHHHHHHHhhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           68 AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        68 ei~~i~~~~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      +++++++++..+.+++++|+.||+.|++.++.-.
T Consensus       263 ~~e~i~~~~~g~~~~g~~K~~lae~i~~~l~pir  296 (341)
T 3sz3_A          263 TFAEIEAQYAGVEMYGPFKKDVGEAVVAMLEPVQ  296 (341)
T ss_dssp             CHHHHHHHTTTCCCSHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6777778887437899999999999999887643

>3prh_A Tryptophanyl-tRNA synthetase; TRPRS, protein biosynthesis, translation, class I tRNA synth rossman fold, high motif, KMSKS motif; 2.80A {Bacillus subtilis}

Probab=99.17  E-value=1.6e-11  Score=114.28  Aligned_cols=89  Identities=18%  Similarity=0.117  Sum_probs=68.8

Q ss_pred             ceeeecccc-------cCC-CC-CccccCC---CCeEeecCCCCCHHHHHHHhhcC-CCh------------h---HHHH
Q psy938            6 DGGLTTPII-------ESE-SG-EKFGKSA---RNAIWLDSKLSSSFELYQYLIRT-KDS------------E---VYDL   57 (241)
Q Consensus         6 ~~~lt~pLL-------~g~-dG-~KmsKS~---gn~I~L~~~~Tsp~~~yq~~~~~-~D~------------~---v~~~   57 (241)
                      .|.+..|+|       +|+ || +|||||.   +|+|||.+   +|+++++|++++ +|+            +   +..|
T Consensus       202 ~f~~p~~li~~~~~~l~gL~dg~~KMSKS~~~~~n~I~L~D---~p~~I~kKI~ka~TD~~~~~~~~~~~~p~v~~l~~i  278 (388)
T 3prh_A          202 IFTIPEVKIPKVGARIMSLNDPLKKMSKSDPNQKAYITLLD---EPKQLEKKIKSAVTDSEGIVKFDKENKPGVSNLLTI  278 (388)
T ss_dssp             CCCCCEECCCSCCCCCBCSSCTTSBCCTTCSSTTSCCBTTC---CHHHHHHHHHTCCCCSSCCCCCCTTTCHHHHHHHHH
T ss_pred             CcccchhhhcccccccccCCCCCCccCCCCCCCCCeeecCC---CHHHHHHHHhhccCCCCCcccCCCCCCCCcchHHHH
Confidence            455555555       677 55 6999999   89999999   999999999998 452            2   5555


Q ss_pred             HHHhcCCCHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhccCHH
Q psy938           58 LKLFSFDSLAAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEE  101 (241)
Q Consensus        58 l~~~t~l~~eei~~i~~~~~~~~~~~~~Kk~LA~~i~~~vhG~~  101 (241)
                      +..|++   ++++++++++. +.+++++|+.||+.|++.+..-.
T Consensus       279 ~~~~~~---~~~eel~~~y~-g~~~g~lK~~lae~l~~~l~pir  318 (388)
T 3prh_A          279 YSILGN---TTIEELEAKYE-GKGYGEFKGDLAEVVVNALKPIQ  318 (388)
T ss_dssp             HHHHHT---CCHHHHHHHTT-TCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCC---CcHHHHHHHHc-CCCHHHHHHHHHHHHHHHHHHHH
Confidence            555554   55677777877 55999999999999999887644

>3n9i_A Tryptophanyl-tRNA synthetase; tryptophan-tRNA ligase, csgid, structural genomics, niaid, center for structural genomics infectious diseases; 1.95A {Yersinia pestis} SCOP: c.26.1.1

Probab=99.17  E-value=1.5e-11  Score=112.96  Aligned_cols=85  Identities=18%  Similarity=0.138  Sum_probs=68.8

Q ss_pred             ccccCC-CC-CccccCCC---CeEeecCCCCCHHHHHHHhhcC-C--------------ChhHHHHHHHhcCCCHHHHHH
Q psy938           12 PIIESE-SG-EKFGKSAR---NAIWLDSKLSSSFELYQYLIRT-K--------------DSEVYDLLKLFSFDSLAAIED   71 (241)
Q Consensus        12 pLL~g~-dG-~KmsKS~g---n~I~L~~~~Tsp~~~yq~~~~~-~--------------D~~v~~~l~~~t~l~~eei~~   71 (241)
                      ++|+|+ || +|||||.+   |+|||++   +|+++++|++++ +              ++.+.+++.+|+.++.+++++
T Consensus       196 ~~l~gL~dg~~KMSKS~~~~~~~I~L~D---~p~~i~kKI~kA~Td~~~~~~~~~~~~~~p~v~~l~~~~~~~~~~~~ee  272 (346)
T 3n9i_A          196 ARVMSLQDPTKKMSKSDDNRNNVIELLE---DPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSGVTGQSIPE  272 (346)
T ss_dssp             CCCBCSSCTTSBCCTTCSCGGGCCBTTS---CHHHHHHHHHTCCCCCCSSCCCCCCTTTCHHHHHHHHHHHHHHCCCHHH
T ss_pred             ccCccCCCCccccCCCCCCCCceecCCC---CHHHHHHHHHhCcCCCCCCccccCCCCCCCChhHHHHHHHhcCCccHHH
Confidence            567788 78 59999997   7999999   999999999997 2              235777777776665567778


Q ss_pred             HHHHhhcCCChHHHHHHHHHHHHhhccCH
Q psy938           72 FKRQNEHKPEERRAQKKLAEDLTLLVHGE  100 (241)
Q Consensus        72 i~~~~~~~~~~~~~Kk~LA~~i~~~vhG~  100 (241)
                      +++++..+ +++++|+.||+.|++.+..-
T Consensus       273 l~~~y~~~-~~g~lK~~lae~l~~~L~pi  300 (346)
T 3n9i_A          273 LEAQFTGQ-MYGHLKGAVADAVSGMLSEL  300 (346)
T ss_dssp             HHHHTTTC-CHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCC-CHHHHHHHHHHHHHHHHHHH
Confidence            88887654 68999999999999887653

>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6

Probab=98.54  E-value=4.5e-08  Score=71.19  Aligned_cols=59  Identities=12%  Similarity=0.107  Sum_probs=48.9

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEE
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANII  211 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~  211 (241)
                      .+++|.++|...|++.|+++|+++|++|.|+|||++++++...+...+        .+.++++.+.+
T Consensus        19 ~~~RLdk~L~~~g~~~SR~~a~~lI~~G~V~VNG~~v~~~~~~v~~gd--------~I~v~~~~~~~   77 (79)
T 1p9k_A           19 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQ--------TVSFAGHSVQV   77 (79)
T ss_dssp             SCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSSE--------EEEETTEEEEE
T ss_pred             CCchHHHHHHHCCCCCCHHHHHHHHHCCEEEECCEEecCCCCCCCCCC--------EEEECCEEEEE
Confidence            357899999999999999999999999999999999989887765431        56777766543

>3p0j_A Tyrosyl-tRNA synthetase; aminoacyl-tRNA synthetase, tRNA ligase, AARS, tyrrs, pseudod translation, ATP-binding, nucleotide-binding, ligase; HET: TYE; 2.89A {Leishmania major} PDB: 3p0i_A* 3p0h_A*

Probab=98.53  E-value=7.7e-08  Score=95.42  Aligned_cols=90  Identities=9%  Similarity=0.008  Sum_probs=72.6

Q ss_pred             eeeecccccCCCC-Ccc-c-cCCCCeEeecCCCCCHHHHHHHhhc------CCChhHHHHHHHhc---------------
Q psy938            7 GGLTTPIIESESG-EKF-G-KSARNAIWLDSKLSSSFELYQYLIR------TKDSEVYDLLKLFS---------------   62 (241)
Q Consensus         7 ~~lt~pLL~g~dG-~Km-s-KS~gn~I~L~~~~Tsp~~~yq~~~~------~~D~~v~~~l~~~t---------------   62 (241)
                      +.+..+++|+++| .|| | +|.+|+|+|++   +|.++++|+++      ++++.+..|++++.               
T Consensus       548 ~~~~~~~~P~L~gp~~~~~~~s~~~~I~l~D---~~~~i~~KI~kA~c~p~ve~np~l~~~~~~~~~~~~~~i~r~~~~G  624 (690)
T 3p0j_A          548 VQTLEGRIPALHRPGAAPAVLGADDVLYLDD---NDMDIRRKIKKAYSAPNEEANPVISVAQHLLAQHGALSIERGEANG  624 (690)
T ss_dssp             EECCCCSSCCSSCCCC-------CCSCBTTC---CHHHHHHHHHHSCCCTTCSCSHHHHHHHHHHHHHSCEEECCCTTTT
T ss_pred             ccccccccccCCCcccccCCCCCCCeeeccC---CHHHHHHHHHHhcCCCCCCCChHHHHHHHHhccCCceEEechhhhC
Confidence            4455678889987 455 4 46799999999   99999999999      58999999999983               


Q ss_pred             -CCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           63 -FDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        63 -~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                       .++.++++++++.+..| .+|+++|..||+.|++++..
T Consensus       625 g~~~~~~~eel~~~y~~G~lhp~dlK~~la~~l~~~l~p  663 (690)
T 3p0j_A          625 GNVSYNTPEALVADCGSGALHPADLKAAVLQLLLDRSAQ  663 (690)
T ss_dssp             CCEEESSHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence             23356899999999888 79999999999999998874

>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.19  E-value=1.4e-06  Score=62.38  Aligned_cols=44  Identities=14%  Similarity=0.123  Sum_probs=41.0

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSP  190 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~  190 (241)
                      .+|..+|+..|+++|+++||++|.+|-|+|||++++.|.+.+..
T Consensus         8 ~RLD~~l~~~gla~SR~~A~~lI~~G~V~Vng~~v~kps~~V~~   51 (71)
T 2cqj_A            8 RRLPTVLLKLRMAQHLQAAVAFVEQGHVRVGPDVVTDPAFLVTR   51 (71)
T ss_dssp             EEHHHHHHHTTCSSSHHHHHHHHHTTCEEETTBCCCCTTCEEEH
T ss_pred             HHHHHHHHHhCCcCCHHHHHHHHHCCcEEECCEEECCCCCCCCC
Confidence            46888999999999999999999999999999999999988765

>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=97.76  E-value=2e-05  Score=66.08  Aligned_cols=46  Identities=13%  Similarity=0.120  Sum_probs=42.4

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|..+|+..|+++|+++|+++|.+|.|+|||++|++|.+.+..+
T Consensus       102 e~RLD~~L~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~  147 (180)
T 3j20_D          102 ERRLQTIVYKKGLARTMRQARQLIVHGHIEVNGQIIRSPSYLVLKE  147 (180)
T ss_dssp             HTSHHHHHHHHTSSSSHHHHHHHHHHTCCEESSSBCCCSSCCCCTG
T ss_pred             hhhhhheeecCcccCcHHHHHHHHHcCCeEECCEEeCCCCcccCCC
Confidence            3678889999999999999999999999999999999999888765

>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C

Probab=97.71  E-value=4.8e-05  Score=62.38  Aligned_cols=46  Identities=15%  Similarity=0.192  Sum_probs=41.5

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.+|..+|...|++.|+++||++|.+|.|.|||+++++|++.+..+
T Consensus        50 e~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VNG~~v~~ps~~V~~g   95 (159)
T 1c05_A           50 ESRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPG   95 (159)
T ss_dssp             HHBHHHHHHHTTSCSSHHHHHHHHHTTCEEETTEECCCSSCBCCTT
T ss_pred             HHHHHHHHHHcCCcCCHHHHHHHHHCCCEEECCEEeCcCCcEeCCC
Confidence            4578999999999999999999999999999999998898877654

>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*

Probab=97.69  E-value=2.7e-05  Score=66.13  Aligned_cols=46  Identities=11%  Similarity=0.010  Sum_probs=42.6

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|..+|+.+|+++|+++|+++|.+|.|+|||++|+.|.+.+..+
T Consensus       106 e~RLD~~L~r~G~a~Sr~~ArqLI~~GhV~VNG~~V~~Ps~~V~~g  151 (197)
T 3u5c_J          106 ERRLQTQVYKLGLAKSVHHARVLITQRHIAVGKQIVNIPSFMVRLD  151 (197)
T ss_dssp             TTSHHHHHHHSSTTSSHHHHHHHHHTSCCBSSSCBCCCTTCCCCST
T ss_pred             HHHHHHHHHHccccCCHHHHHHHHHcCCEEECCEEeCCCccccCCC
Confidence            4678899999999999999999999999999999999999888765

>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D

Probab=97.58  E-value=6.2e-05  Score=63.11  Aligned_cols=46  Identities=9%  Similarity=0.021  Sum_probs=42.7

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|..+|+..|++.|+++|+++|.+|-|.|||+.|++|.+.+..+
T Consensus       106 e~RLD~vL~~~G~a~SR~~Ar~LI~~G~V~VNg~~V~~Ps~~V~~~  151 (181)
T 2xzm_D          106 ERRLQTRVFKLNLANSIHHSRVLIRQRHIKVGKNLVNVPSFMVRTD  151 (181)
T ss_dssp             TTBHHHHHHHTTCSSSTTHHHHHTTTTCCEETTEECCCSCCBCCST
T ss_pred             ccchhHHHHhccccCCHHHHHHHHHCCEEEECCEEECCCCcCCCCC
Confidence            4689999999999999999999999999999999999999988765

>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...

Probab=97.25  E-value=0.00042  Score=59.18  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=41.4

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +++|..+|...|++.|+++|+++|.+|.|.|||++++.|++.+...
T Consensus        98 e~RLD~~L~~~g~~~SR~~arqLI~~G~V~VNG~~v~~ps~~V~~g  143 (209)
T 2vqe_D           98 ESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPG  143 (209)
T ss_dssp             HTBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTT
T ss_pred             HHHHHHHHHHhcCcCCHHHHHHHHHCCCEEECCEEeCcCCcCcCCC
Confidence            3678899999999999999999999999999999998898877654

>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A

Probab=97.24  E-value=0.0017  Score=51.59  Aligned_cols=65  Identities=14%  Similarity=0.113  Sum_probs=49.3

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEccc
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANI  217 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~~~  217 (241)
                      .+++|..+|...+++.|++.|+++|.+|.|+|||+.+ .+...+...      ..+.|+.+... +.++..++
T Consensus         7 ~~~RLDk~L~~~~~~~SRs~a~~li~~G~V~VNG~~v-k~s~~V~~G------D~I~I~~~~~~-~~~~v~~~   71 (133)
T 1dm9_A            7 VEVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRS-KPSKIVELN------ATLTLRQGNDE-RTVIVKAI   71 (133)
T ss_dssp             TCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEEC-CTTCBCCTT------CEEEEEETTEE-EEEEECEE
T ss_pred             cchhHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEc-CCCCEeCCC------CEEEEEeCCce-eeEEEccc
Confidence            3678999999988888999999999999999999986 777766544      34566666544 34444443

>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}

Probab=96.93  E-value=0.00033  Score=59.56  Aligned_cols=45  Identities=18%  Similarity=0.151  Sum_probs=39.7

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..+|...|++.|+++||++|.+|.|.|||+.++.|.+.+...
T Consensus        89 ~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VNG~~V~~pS~~V~~g  133 (201)
T 3bbn_D           89 MRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQ  133 (201)
T ss_dssp             SBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTT
T ss_pred             HHHHHHHHHcCCcCCHHHHHHHHhCCcEEeCCEEEeecceecCCC
Confidence            456667888899999999999999999999999999998877654

>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}

Probab=96.86  E-value=0.00085  Score=59.94  Aligned_cols=46  Identities=13%  Similarity=0.109  Sum_probs=40.9

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEcc-E-EecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNY-K-KVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg-~-~v~d~~~~l~~~  191 (241)
                      .++|..+|++.|++.|+++|+++|.+|.|+||| + ++++|...+...
T Consensus         6 ~~RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vng~~~~v~kp~~~V~~~   53 (291)
T 3hp7_A            6 KERVDVLAYKQGLFETREQAKRGVMAGLVVNVINGERYDKPGEKIDDG   53 (291)
T ss_dssp             EEEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTTCCBCCCTTCEEETT
T ss_pred             hhhHHHHHHHcCCcccHHHHHHHHHCCeEEECCeEEEEccCCCCCCCC
Confidence            357899999999999999999999999999999 8 788888777544

>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}

Probab=96.69  E-value=0.00093  Score=49.19  Aligned_cols=43  Identities=9%  Similarity=0.044  Sum_probs=36.0

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +|..+|...+++.|++.++++|.+|.|+|||+.+ .++..+..+
T Consensus         2 RLD~~L~~~~~~~sR~~~~~li~~G~V~VNg~~~-~~~~~v~~g   44 (92)
T 2k6p_A            2 RIDKFLQSVGLVKRRVLATDMCNVGAVWLNGSCA-KASKEVKAG   44 (92)
T ss_dssp             BHHHHSTTTTSCCCCCSSCCHHHHTCCEETTEEC-CTTCBCCTT
T ss_pred             hHHHHHHHCCCCCCHHHHHHHHHCCcEEECCEEc-CCCCCcCCC
Confidence            4677888888888999999999999999999987 677766544

>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=96.41  E-value=5.5e-05  Score=64.09  Aligned_cols=46  Identities=13%  Similarity=0.080  Sum_probs=41.7

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|..+|+.+|+++|+++|+++|.+|-|.|||++|+.|.+.+..+
T Consensus       108 e~RLD~~L~r~G~a~SR~~ArqlI~~GhV~VNG~~V~~Ps~~V~~g  153 (195)
T 3iz6_C          108 ARRLQTLVFKAGMAKSIHHARVLIRQRHIRVGRQIVNIPSFMVRVE  153 (195)
T ss_dssp             TSCCCSSCCCCCCHHHHSCTTSHHHHHSTTTSCCCCCCCCCCCSSS
T ss_pred             HhhhhHHHHhccccCCHHHHHHHHHcCCEEECCEEeCCCCcCcCCC
Confidence            3567778999999999999999999999999999999999988765

>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}

Probab=96.30  E-value=0.0044  Score=55.26  Aligned_cols=45  Identities=16%  Similarity=0.282  Sum_probs=39.4

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+++|..+|...|.+ |+++|+++|.+|.|+|||+.+ +++..+...
T Consensus         5 ~g~RLdk~La~~g~~-SR~~a~~lI~~G~V~VNG~~v-~~~~~V~~g   49 (290)
T 3dh3_A            5 SSVRLNKYISESGIC-SRREADRYIEQGNVFLNGKRA-TIGDQVKPG   49 (290)
T ss_dssp             CCEEHHHHHHTTTSS-CHHHHHHHHHTTCEEETTEEC-CTTCEECTT
T ss_pred             cchHHHHHHHhCCCC-CHHHHHHHHHCCCEEECCEEc-cCCcCcCCC
Confidence            367899999999887 999999999999999999988 777777654

>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*

Probab=95.85  E-value=0.0073  Score=51.58  Aligned_cols=45  Identities=18%  Similarity=0.028  Sum_probs=38.1

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +++|.++|...+ .-|+++++++|.+|.|+|||+++++++..+...
T Consensus         3 ~~RLd~~L~~~~-~~SR~~~~~li~~G~V~VNG~~v~~~~~~v~~g   47 (234)
T 1ksk_A            3 HMRLDKFIAQQL-GVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPE   47 (234)
T ss_dssp             CEEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTT
T ss_pred             cccHHHHHHHcC-CCCHHHHHHHHHcCeEEECCEEeCCCCCCCCCC
Confidence            457888998776 459999999999999999999998788777654

>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5

Probab=95.43  E-value=0.013  Score=50.49  Aligned_cols=44  Identities=11%  Similarity=0.063  Sum_probs=36.9

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++|.++|...+ ..|+++++++|.+|.|+|||+++++++..+...
T Consensus         3 ~RLd~~L~~~~-~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g   46 (243)
T 1vio_A            3 LRLDKFIAENV-GLTRSQATKAIRQSAVKINGEIVKSGSVQISQE   46 (243)
T ss_dssp             EEHHHHHHHHH-TCCHHHHHHHHHTTCEEETTEECCCTTCEECTT
T ss_pred             ccHHHHHHHcC-CCCHHHHHHHHHcCcEEECCEEeCCCCCCcCCC
Confidence            46788888776 459999999999999999999988787777654

>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}

Probab=95.34  E-value=0.048  Score=47.48  Aligned_cols=73  Identities=14%  Similarity=0.133  Sum_probs=52.2

Q ss_pred             CCcHHHHHH-hcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCccc-----CCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSL-ATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHIL-----PNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv-~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~-----~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      ..+|.=+|. ..|++.+.+|||+.+.||-|.|||.+++|+.+.+..- |++     ...|-++---|.+|.+..+....|
T Consensus        42 ~lPL~i~LRdrLgyA~t~rEar~Iv~~~~I~VdGKvr~d~~ypvG~m-DVIsI~kt~e~fr~i~d~kGr~~~~~I~~eea  120 (243)
T 3j20_E           42 SIPLLYIVRDYLGYAKTAREARKILNEGKFLVDGRVRKDYKFPVGIM-DVVSIPETGEHYRVLPNRIGKLILHPISEDEA  120 (243)
T ss_dssp             CEEHHHHHHTTSCCCSSHHHHHHHHHHCSCEETTEECCCSSCEECTT-CEEEETTTTEEEEEEECSSSCEEEEEECTTTT
T ss_pred             ceeehhhhhhhhccccCHHHHHHHHHCCcEEECCEEeccccCCcccc-eEEEecccCceeEEEecCCCceEEEEeChhhc
Confidence            467777777 4799999999999999999999999999998876543 221     223445554455555555555555

>2d5b_A Methionyl-tRNA synthetase; rossmann fold, class 1A AARS, isomerase, structural genomics, NPPSFA; 1.80A {Thermus thermophilus} SCOP: a.27.1.1 c.26.1.1 PDB: 1woy_A 1a8h_A 2d54_A

Probab=95.26  E-value=0.0048  Score=58.14  Aligned_cols=27  Identities=15%  Similarity=-0.002  Sum_probs=22.6

Q ss_pred             eeeecccccCCCCCccccCCCCeEeec
Q psy938            7 GGLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         7 ~~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      ..++...++..+|+|||||.||+|++.
T Consensus       283 ~v~~~G~v~~~~G~KMSKS~GN~i~p~  309 (500)
T 2d5b_A          283 HLNVGGFLLGPDGRKMSKTLGNVVDPF  309 (500)
T ss_dssp             EEEEECCEECTTSSCCCTTTTCCCCHH
T ss_pred             EEEECceEEeCCCCcccccCCCCCCHH
Confidence            346678888889999999999999765

>1irx_A Lysyl-tRNA synthetase; beta sandwitch, zinc-binding structure, rossmann fold, alpha-helix CAGE; 2.60A {Pyrococcus horikoshii} SCOP: a.97.1.2 c.26.1.1

Probab=94.76  E-value=0.015  Score=55.55  Aligned_cols=45  Identities=16%  Similarity=0.067  Sum_probs=26.6

Q ss_pred             CceeeecccccCC-CCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            5 GDGGLTTPIIESE-SGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         5 ~~~~lt~pLL~g~-dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      +++-++.|+|++. +|+|||||.||+|++.+  ++-.|+.+.-|+.+.
T Consensus       262 ~p~~~h~~~i~~~g~g~KmSKs~Gn~i~~~~~~~~~~pdalR~~l~~~  309 (523)
T 1irx_A          262 APLSLMYEFVGIKGQKGKMSGSKGNVILLSDLYEVLEPGLVRFIYARH  309 (523)
T ss_dssp             CCBCCEECCEEESCC---------CCCCHHHHHTTSCHHHHHHHHHSS
T ss_pred             CCeEEEEEEEEeCCCCCCCCCcCCCCCCHHHHHHHcCHHHHHHHHHhc
Confidence            4466788999888 79999999999986652  226888888888873

>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}

Probab=94.71  E-value=0.055  Score=46.23  Aligned_cols=46  Identities=17%  Similarity=0.182  Sum_probs=38.8

Q ss_pred             CCcHHHHHH-hcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSL-ATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv-~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|.=+|. ..|++.+.+|||+.+.||-|.|||.+++||.+.+..-
T Consensus         7 slPL~i~LRdrLgyA~t~rEarkIv~~~~I~VDGKvr~d~~ypvG~m   53 (213)
T 3kbg_A            7 SVTLLSIIRDYLKLSDKEREAARILANGLVKVDGKTVREKKFAVGFM   53 (213)
T ss_dssp             CEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEETTEECCCTTCEECTT
T ss_pred             ceeeHHHHhhhhcccccHHHHHHHHHCCCEEECCEEecccCCCccce
Confidence            456766776 4799999999999999999999999999998866543

>3u1f_A Methionyl-tRNA synthetase; aminoacyl-tRNA synthetase, AARS, metrs, parasite, protein-IN complex, rossmann-fold, translation; HET: 392; 2.20A {Trypanosoma brucei} PDB: 3u1e_A* 3u1g_A* 3u20_A* 4eg1_A 4eg3_A* 4eg6_A* 4eg8_A* 4eg5_A* 3tun_A* 3u1z_A* 4eg4_A* 4eg7_A* 4ega_A*

Probab=94.54  E-value=0.021  Score=54.23  Aligned_cols=18  Identities=22%  Similarity=0.108  Sum_probs=15.2

Q ss_pred             CCCCCccccCCCCeEeec
Q psy938           16 SESGEKFGKSARNAIWLD   33 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~   33 (241)
                      ..+|+|||||.||+|+..
T Consensus       318 ~~~G~KMSKSlGNvi~p~  335 (542)
T 3u1f_A          318 TKDRKKISKSLGNVFDPV  335 (542)
T ss_dssp             EETTBCCBTTTTBCCCHH
T ss_pred             ecCCceeccccCCCCChh
Confidence            358999999999998654

>1gax_A Valrs, valyl-tRNA synthetase; protein-RNA complex, rossmann fold, coiled coil, riken structural genomics/proteomics initiative, RSGI; HET: VAA; 2.90A {Thermus thermophilus} SCOP: a.2.7.3 a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1ivs_A* 1iyw_A

Probab=94.49  E-value=0.012  Score=59.82  Aligned_cols=41  Identities=27%  Similarity=0.137  Sum_probs=29.3

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++..++.+.+|+|||||.||.|+..+  ++-.++.++=++++
T Consensus       515 v~~hG~vld~~G~KMSKSlGNvIdP~dli~~yGaDalR~~ll~  557 (862)
T 1gax_A          515 VLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIY  557 (862)
T ss_dssp             EEEECCEECTTSCBCCTTTTCCCCHHHHHHHHCHHHHHHHHHH
T ss_pred             EEEeeeEEcCCCCCccccCCCCCCHHHHHHHcChHHHHHHHHh
Confidence            556778889999999999999997652  11245555555555

>2csx_A Methionyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiative, RSGI, structural genomics, ligase/RNA complex; 2.70A {Aquifex aeolicus} PDB: 2ct8_A*

Probab=94.44  E-value=0.0083  Score=56.56  Aligned_cols=40  Identities=18%  Similarity=0.122  Sum_probs=25.9

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++...++. +|+|||||.||+|++.+  +.-.++.++=++++
T Consensus       283 ~~~~G~v~~-~G~KMSKS~GN~i~~~dli~~~g~DalR~~ll~  324 (497)
T 2csx_A          283 VFAHGWWTV-EGKKMSKTLGNVVDPYEVVQEYGLDEVRYFLLR  324 (497)
T ss_dssp             EEEECCEES-SSSBCCTTTTCCCCHHHHHHHHCHHHHHHHHHH
T ss_pred             EEECcEEEe-CCceeCCcCCCCCCHHHHHHHCCcHHHHHHHHh
Confidence            345566665 99999999999997663  11234445545544

>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A

Probab=93.84  E-value=0.011  Score=53.14  Aligned_cols=46  Identities=15%  Similarity=-0.004  Sum_probs=0.0

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +++|.++|...+...|+++++++|.+|.|+|||+++..++..+..+
T Consensus        16 g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VNG~~v~~~~~~v~~g   61 (325)
T 1v9f_A           16 GQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGG   61 (325)
T ss_dssp             ----------------------------------------------
T ss_pred             CchHHHHHHhhccccCHHHHHHHHHCCCEEECCEEccCCCCEeCCC
Confidence            6788999988775569999999999999999999877777666544

>1ile_A Ilers, isoleucyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics; 2.50A {Thermus thermophilus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1jzq_A* 1jzs_A*

Probab=93.84  E-value=0.014  Score=58.74  Aligned_cols=41  Identities=22%  Similarity=0.163  Sum_probs=29.2

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++...+.+.+|+|||||.||.|+..+  ++-.++.++=++++
T Consensus       578 v~~hg~vl~~~G~KMSKS~GNvV~p~dli~~yGaDalR~~ll~  620 (821)
T 1ile_A          578 VICHGLILDEKGQKMSKSKGNVVDPWDIIRKFGADALRWYIYV  620 (821)
T ss_dssp             EEEECCEECTTSSCCCTTTTCCCCHHHHHTTTCHHHHHHHHHH
T ss_pred             EEEEeeEECCCCCCCCccCCCCCCHHHHHHHhCHHHHHHHHHh
Confidence            456677788899999999999997662  23455555555554

>1ffy_A Isoleucyl-tRNA synthetase; protein-RNA complex, metal IONS, editing tRNA synthetase, double-sieve, ligase/RNA, mupiroci; HET: MRC; 2.20A {Staphylococcus aureus} SCOP: a.27.1.1 b.51.1.1 c.26.1.1 PDB: 1qu2_A* 1qu3_A*

Probab=93.45  E-value=0.037  Score=56.49  Aligned_cols=42  Identities=24%  Similarity=0.185  Sum_probs=29.7

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      .++...+.+.+|+|||||.||.|+..+  ++-.++.++=++++.
T Consensus       582 v~~hG~V~d~~G~KMSKSlGNvV~P~dvi~~yGaDalR~~lls~  625 (917)
T 1ffy_A          582 LLSHGFVMDGEGKKMSKSLGNVIVPDQVVKQKGADIARLWVSST  625 (917)
T ss_dssp             EEEECCEECTTSCCCCSSSSCCCCHHHHHHHTCHHHHHHHHHTS
T ss_pred             eeEeeeEEcCCCcCcccccCCcCChHHHHHhCCHHHHHHHHhcc
Confidence            355577888899999999999997652  123555666566653

>3kfl_A Methionyl-tRNA synthetase; parasite, aminoacyl-tRNA synthetase, tRNA ligase metrs, methionine, translation, ATP-binding; HET: ME8; 2.00A {Leishmania major}

Probab=93.14  E-value=0.014  Score=56.20  Aligned_cols=38  Identities=24%  Similarity=0.107  Sum_probs=25.2

Q ss_pred             ecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           10 TTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      +...+ +.+|+|||||.||+|++.+  +.-.++.++=++++
T Consensus       329 ~hg~v-~~~G~KMSKS~GNvV~p~d~i~~~G~DalR~~ll~  368 (564)
T 3kfl_A          329 SHGWW-TKDHKKISKSLGNAFDPVEKAKEFGIDALKYFLMR  368 (564)
T ss_dssp             EECCE-EETTEECCTTTTCCCCHHHHHHHHCHHHHHHHHHH
T ss_pred             EcccE-eeCCccccccCCCCCCHHHHHHHcCcHHHHHHHHH
Confidence            34445 6799999999999998753  12345555545554

>4dlp_A Aminoacyl-tRNA synthetase, class I:aminoacyl-tRNA synthetase, class IA:methionyl-tRNA...; structural genomics; 2.65A {Brucella melitensis biovar abortus 230ORGANISM_TAXID}

Probab=93.11  E-value=0.015  Score=55.52  Aligned_cols=24  Identities=29%  Similarity=0.239  Sum_probs=6.8

Q ss_pred             eecccccCCCCCccccCCCCeEeec
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      ++...++. +|+|||||.||+|++.
T Consensus       310 ~~hg~v~~-~G~KMSKS~GNvi~p~  333 (536)
T 4dlp_A          310 FAHGFLFN-RGEKMSKSVGNVIDPF  333 (536)
T ss_dssp             EEECCEEC-------------CCHH
T ss_pred             EeeeeEee-CCceecccCCCCCCHH
Confidence            34455553 9999999999999775

>1li5_A Cysrs, cysteinyl-tRNA synthetase, transfer RNA-Cys; cysteine, E.coli, ligase; 2.30A {Escherichia coli} SCOP: a.27.1.1 c.26.1.1 PDB: 1li7_A 1u0b_B

Probab=93.10  E-value=0.031  Score=52.62  Aligned_cols=40  Identities=18%  Similarity=0.210  Sum_probs=29.1

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ++...|+. +|+|||||.||.|++.+  ++-+|..++=++++.
T Consensus       255 ~h~g~v~~-~G~KMSKS~GN~v~~~dll~~~g~dalR~~ll~~  296 (461)
T 1li5_A          255 MHSGMVMV-DREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSG  296 (461)
T ss_dssp             CCBCCEEE-TTBCCCGGGTCCCBHHHHHTTSCHHHHHHHHHSS
T ss_pred             EEeeEEEE-CCeEccccCCCccChhHHhhhCCHHHHHHHHHcC
Confidence            33344443 89999999999999873  345788887777765

>3c8z_A Cysteinyl-tRNA synthetase; cysteine ligase, rossmann fold, Cys-SA inhibitor, zinc binding, ATP-binding, aminoacyl-tRNA synthetase; HET: 5CA 1PE EPE; 1.60A {Mycobacterium smegmatis}

Probab=93.03  E-value=0.013  Score=54.26  Aligned_cols=18  Identities=28%  Similarity=0.366  Sum_probs=3.6

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      .+|+|||||.||.|++.+
T Consensus       287 ~~G~KMSKS~GN~v~~~~  304 (414)
T 3c8z_A          287 WDGHKMSKSRGNLVLVSQ  304 (414)
T ss_dssp             -------------CBHHH
T ss_pred             cCCeEcccccCCcCCHHH
Confidence            489999999999998763

>3tqo_A Cysteinyl-tRNA synthetase; protein synthesis, ligase; 2.30A {Coxiella burnetii}

Probab=92.86  E-value=0.068  Score=50.58  Aligned_cols=37  Identities=27%  Similarity=0.169  Sum_probs=25.2

Q ss_pred             cccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938           13 IIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus        13 LL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      .+.+.+|+|||||.||.|.+.+  +.-+|..++=++++.
T Consensus       261 g~v~~~G~KMSKSlGN~i~~~dll~~~g~dalR~~lls~  299 (462)
T 3tqo_A          261 GLLEINKEKMSKSLGNIISIREALKESDVEVLRYFLLSG  299 (462)
T ss_dssp             CCEEETTEECCTTTTCCCBHHHHHHHSCHHHHHHHHHHS
T ss_pred             cEEecCCcCccccCCCcccHHHHHhhcChHHhhhhhccC
Confidence            4456799999999999987652  123566665555554

>2x1l_A Methionyl-tRNA synthetase; nucleotide-binding, protein biosynthesis, ligase, aminoacyl- synthetase; HET: ADN CXS; 2.30A {Mycobacterium smegmatis} PDB: 2x1m_A*

Probab=92.63  E-value=0.014  Score=55.39  Aligned_cols=36  Identities=22%  Similarity=0.193  Sum_probs=22.7

Q ss_pred             ccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           12 PIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      ..++. +|+|||||.||+|++.+  ++-.++.++=++++
T Consensus       302 G~v~~-~G~KMSKS~GN~v~p~d~i~~~g~DalR~~ll~  339 (524)
T 2x1l_A          302 GWLLN-RGEKMSKSIGNVVDPVNLVDTFGLDQVRYFLLR  339 (524)
T ss_dssp             CCEEE-CSCSEETTTEESSCHHHHHHHHCHHHHHHHHHH
T ss_pred             cEEEe-CCcccCCcCCCCCCHHHHHHHcChHHHHHHHHh
Confidence            44444 89999999999997763  01234444444444

>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A {Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1

Probab=92.57  E-value=0.017  Score=57.34  Aligned_cols=40  Identities=25%  Similarity=0.359  Sum_probs=29.7

Q ss_pred             eecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~~   49 (241)
                      ++...|+. +|+|||||.||+|+.++  ++-.++.++=|+++.
T Consensus       333 ~~hG~v~~-~G~KMSKS~GNvV~p~d~i~~ygaDalR~~ll~~  374 (722)
T 1rqg_A          333 PANEYLTL-EGKKFSTSRNWAIWVHEFLDVFPADYLRYYLTTI  374 (722)
T ss_dssp             CEECCEEE-TTEECBTTTTBSCBHHHHTTTSCHHHHHHHHHHT
T ss_pred             EEeeeEEe-CCeeeeeeCCCcCCHHHHHHhcCchHHHHHHHhc
Confidence            34445555 99999999999999872  345777887777775

>1wkb_A Leucyl-tRNA synthetase; leucine, aminoacyl-tRNA, editing, amino acid, aminoacylation, trnaLeu, structural genomics; 2.05A {Pyrococcus horikoshii}

Probab=92.56  E-value=0.028  Score=56.34  Aligned_cols=25  Identities=20%  Similarity=0.089  Sum_probs=18.5

Q ss_pred             eeecccccCCCCCccccCCCCeEeec
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLD   33 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~   33 (241)
                      .++...++. +|+|||||.||.|+..
T Consensus       638 v~~~G~v~~-~G~KMSKS~GNvv~p~  662 (810)
T 1wkb_A          638 IAVNGFGTL-EGQKMSKSKGNVLNFI  662 (810)
T ss_dssp             EEEECCEEE-TTBCCCTTTTCCCBHH
T ss_pred             EEEEeEEEe-CCeehhhcCCCcCCHH
Confidence            344444443 8999999999999665

>3h99_A Methionyl-tRNA synthetase; rossmann fold, aminoacyl-tRNA synthetase, ATP-binding, ligas binding, nucleotide-binding, protein biosynthesis; HET: CIT; 1.40A {Escherichia coli} PDB: 3h97_A* 3h9b_A* 1f4l_A 3h9c_A* 1pfv_A* 1pfu_A 1p7p_A* 1pfw_A* 1pfy_A* 1pg0_A* 1pg2_A* 1qqt_A 1mea_A 1med_A

Probab=92.51  E-value=0.025  Score=54.25  Aligned_cols=31  Identities=23%  Similarity=0.179  Sum_probs=21.5

Q ss_pred             CCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           18 SGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        18 dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      +|+|||||.||+|++++  ++-.++.++=++++
T Consensus       342 ~G~KMSKS~GNvv~p~d~i~~~GaDalR~~ll~  374 (560)
T 3h99_A          342 NGAKMSKSRGTFIKASTWLNHFDADSLRYYYTA  374 (560)
T ss_dssp             TTEECCTTTTCCCBHHHHHHHSCHHHHHHHHHH
T ss_pred             CCeeccccCCCcCCHHHHHHHcCcHHHHHHHHH
Confidence            99999999999998763  12345555555544

>1wz2_A Leucyl-tRNA synthetase; ligase, riken structural genomics/proteomics initiativ structural genomics, ligase-RNA complex; 3.21A {Pyrococcus horikoshii}

Probab=92.41  E-value=0.029  Score=57.51  Aligned_cols=40  Identities=15%  Similarity=0.108  Sum_probs=27.6

Q ss_pred             eeecccccCCCCCccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .++.-.+.. +|+|||||.||+|+..+  ++-.++.++=+++.
T Consensus       638 v~~~G~v~~-~G~KMSKS~GNvv~p~d~i~~yGaDalR~~ll~  679 (967)
T 1wz2_A          638 IAVNGFGTL-EGQKMSKSKGNVLNFIDAIEENGADVVRLYIMS  679 (967)
T ss_dssp             EEEECCEEE-SSSCCCTTTCCCCBHHHHHHTTCHHHHHHHHHH
T ss_pred             EEEeeEEee-CCEEccccccCCCCHHHHHHHhChHHHHHHHHh
Confidence            344444554 89999999999998762  23467777766654

>3sp1_A Cysteinyl-tRNA synthetase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, LYME disease; HET: AMP; 2.55A {Borrelia burgdorferi}

Probab=92.12  E-value=0.018  Score=55.09  Aligned_cols=33  Identities=18%  Similarity=0.140  Sum_probs=13.8

Q ss_pred             CCCCccccCCCCeEeecC--CC-CCHHHHHHHhhcC
Q psy938           17 ESGEKFGKSARNAIWLDS--KL-SSSFELYQYLIRT   49 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~--~~-Tsp~~~yq~~~~~   49 (241)
                      .+|+|||||.||.|.+.+  ++ -+|..++=++++.
T Consensus       295 ~~G~KMSKSlGN~it~~dll~~gyg~d~lR~~lls~  330 (501)
T 3sp1_A          295 MDYNKMSKSRGNFITVKDLEDQNFSPLDFRYLCLTS  330 (501)
T ss_dssp             CC----------CCCHHHHHHTTCCHHHHHHHHHTS
T ss_pred             eCCeEccccCCCcCCHHHHHhcCCCHHHHHHHHHhc
Confidence            599999999999987763  12 4566666555554

>1nzj_A Hypothetical protein YADB; Zn cluster, glutamyl T-RNA synthetase, structural genomics, unknown function; 1.50A {Escherichia coli} SCOP: c.26.1.1 PDB: 2zlz_A* 4a91_A*

Probab=90.07  E-value=0.1  Score=46.49  Aligned_cols=28  Identities=18%  Similarity=0.236  Sum_probs=10.4

Q ss_pred             ceeeecccccCCCCCccccCCCCeEeecC
Q psy938            6 DGGLTTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus         6 ~~~lt~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      +.-...|+|.+.+|+||||+.||. .|++
T Consensus       213 p~~~H~pll~~~~g~KLSKR~g~~-~v~~  240 (298)
T 1nzj_A          213 PDYIHLPLALNPQGAKLSKQNHAP-ALPK  240 (298)
T ss_dssp             CEEEEECBCCC--------------CCCS
T ss_pred             CeEEEeeeeECCCCCcccccCCcc-Chhc
Confidence            333789999999999999999987 4543

>2cfo_A Glutamyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase, ATP-binding, nucleotide-B; HET: GLU; 2.45A {Synechococcus elongatus}

Probab=89.93  E-value=0.16  Score=48.42  Aligned_cols=45  Identities=20%  Similarity=0.166  Sum_probs=34.7

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeec---CCCCCHHHHHHHhhcC
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLD---SKLSSSFELYQYLIRT   49 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~---~~~Tsp~~~yq~~~~~   49 (241)
                      ..+.-...|+|.+.+|+||||+.||. .|.   +.--.|..+..|+..+
T Consensus       230 ~~P~~~H~plil~~~g~KLSKr~g~~-~l~~~r~~G~~peal~~~l~~l  277 (492)
T 2cfo_A          230 TPPNFAHTPLILNSTGQKLSKRDGVT-SISDFRAMGYLAPALANYMTLL  277 (492)
T ss_dssp             CCCEEEEECCEECSSSSBCCTTSSCC-BHHHHHHTTCCHHHHHHHHHHT
T ss_pred             CCceEEEeeeEECCCCCEecccCCcc-cHHHHHHCCCCHHHHHHHHHHh
Confidence            34455689999999999999999986 333   2334788898888876

>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=89.63  E-value=0.57  Score=41.14  Aligned_cols=73  Identities=10%  Similarity=-0.054  Sum_probs=52.4

Q ss_pred             CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      ..+|.=+|.. .+.+.+.+||++.+.||-|.|||...+|+.+-+-.= |+     ....|-+|---|.+|.+.++..+-|
T Consensus        41 slPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~M-DVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA  119 (265)
T 3iz6_D           41 CLPLILIIRNRLKYALTYREVISILMQRHVLVDGKVRTDKTYPAGFM-DVISIPKTGENYRLLYDTKGRFRLQSVKDEDA  119 (265)
T ss_dssp             --CHHHHHHHHHTTSSCSSSTHHHHHTTCCEETTEECCCTTCCCCTT-CEEECCSSCCEEEEEECTTSCEEEEEECHHHH
T ss_pred             heeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCcEE-EEEEEcCCCCEEEEEECCCCcEEEEECChHHc
Confidence            5677777764 699999999999999999999999999987655321 11     1234556666677777777766555

>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W

Probab=88.17  E-value=1.1  Score=39.23  Aligned_cols=73  Identities=10%  Similarity=0.078  Sum_probs=52.3

Q ss_pred             CCcHHHHHH-hcCCCCCHHHHHHHHHh--CCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEccc
Q psy938          146 GMSMLELSL-ATKCFPRDKEANLTISE--GGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANI  217 (241)
Q Consensus       146 ~~~l~~lLv-~~gl~~SksEARRlI~q--GgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~  217 (241)
                      ..+|.=+|. ..+.+.+.+|||+.+.|  |-|.|||...+|+.+-+-.= |+     ....|-+|---|.+|.+.+...+
T Consensus        41 slPL~i~LRd~LkyA~t~rEak~Il~q~~~~VkVDGkvr~D~~~PvG~M-DVIsI~kt~e~fRll~D~kGrf~l~~I~~e  119 (260)
T 2xzm_W           41 SLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVDGKVRRDKGYPTGLM-DVVRIEKTDQSFRILYDTKGRFVLKSLSKE  119 (260)
T ss_dssp             CEEHHHHHTTTTCSCCSHHHHHHHTTSTTCCEEETTEECCCTTCEECTT-CEEEEGGGTEEEEEEECSSSCEEEEECCTT
T ss_pred             eehhHhhhhhhhccccchhHHHHHHhccCCeEEECCEEeccCCCCCcEE-EEEeEcCCCCEEEEEEcCCccEEEEEcChH
Confidence            467777776 46899999999999999  99999999999987655322 11     12334456556666777776655


Q ss_pred             ch
Q psy938          218 IA  219 (241)
Q Consensus       218 ~~  219 (241)
                      -|
T Consensus       120 EA  121 (260)
T 2xzm_W          120 EA  121 (260)
T ss_dssp             GG
T ss_pred             Hc
Confidence            55

>3fnr_A Arginyl-tRNA synthetase; transferase, PSI-2, NYSGXRC, struc genomics, protein structure initiative; 2.20A {Campylobacter jejuni}

Probab=83.97  E-value=0.17  Score=47.81  Aligned_cols=26  Identities=27%  Similarity=0.420  Sum_probs=16.7

Q ss_pred             eecccc-cCCCCC--ccccCCCCeEeecC
Q psy938            9 LTTPII-ESESGE--KFGKSARNAIWLDS   34 (241)
Q Consensus         9 lt~pLL-~g~dG~--KmsKS~gn~I~L~~   34 (241)
                      ++..++ .+.||+  |||||.||+|++++
T Consensus       270 ~~~g~V~l~~dG~~~KMSKr~Gn~v~l~d  298 (464)
T 3fnr_A          270 ILAQMVSLLKDGEPYKMSKRAGNFILMSD  298 (464)
T ss_dssp             EEECCEEEEETTEECCC---CCSSCBHHH
T ss_pred             EEeeeEEecCCCcccCCcCcCCCCCCHHH
Confidence            445555 456885  99999999998774

>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E

Probab=83.74  E-value=0.55  Score=41.15  Aligned_cols=73  Identities=8%  Similarity=0.003  Sum_probs=48.9

Q ss_pred             CCcHHHHHHh-cCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcc-----cCCCeEEEEeccccEEEEEEcccch
Q psy938          146 GMSMLELSLA-TKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHI-----LPNSLTLLRVEVSANIIAKSANIIA  219 (241)
Q Consensus       146 ~~~l~~lLv~-~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~-----~~~~~~llr~GKk~~~~i~~~~~~~  219 (241)
                      ..+|.=+|.. .+.+.+.+||++.+.||-|.|||...+|+.+-+-.= |+     ....|-+|---|.+|.+.+...+-|
T Consensus        41 slPL~i~LRd~LkyA~t~~EakkIl~q~~VkVDGkvrtD~~~PvG~M-DVIsI~kt~e~fRll~D~kGrf~l~~I~~eEA  119 (261)
T 3u5c_E           41 SLPLIVFLRNRLKYALNGREVKAILMQRHVKVDGKVRTDTTYPAGFM-DVITLDATNENFRLVYDVKGRFAVHRITDEEA  119 (261)
T ss_dssp             EEEHHHHHHHTTCCCSSSHHHHHHHTTTCEEETTBCCCCTTCEEETT-CEEEETTTTEEEECCBCSSSCBCCEECCTTGG
T ss_pred             heeeHHHhhhhhcccccHHHHHHHHHCCcEEECCEEeccCCCCCceE-EEEEEcCCCCEEEEEECCCCcEEEEECChHHc
Confidence            4577777764 699999999999999999999999999987644221 11     1122334444455555555554444

>4arc_A Leucine--tRNA ligase; ligase-RNA complex, nucleotide-binding, protein biosynthesis I aminoacyl-tRNA synthetase, ATP-binding; 2.00A {Escherichia coli} PDB: 4aq7_A 4ari_A* 4as1_A*

Probab=82.44  E-value=0.65  Score=47.22  Aligned_cols=13  Identities=38%  Similarity=0.315  Sum_probs=11.3

Q ss_pred             ccccCCCCeEeec
Q psy938           21 KFGKSARNAIWLD   33 (241)
Q Consensus        21 KmsKS~gn~I~L~   33 (241)
                      |||||.||.|..+
T Consensus       639 KMSKSkGNvVdP~  651 (880)
T 4arc_A          639 KMSKSKNNGIDPQ  651 (880)
T ss_dssp             ECCTTTTCCCCHH
T ss_pred             cccCcCCCCCCHH
Confidence            9999999998544

>4g6z_A Glutamate-tRNA ligase; aminoacyl-tRNA synthetase, AARS, class 1B AARS, ATP-dependen charging, protein synthesis, structural genomics; HET: GLU; 2.05A {Burkholderia thailandensis}

Probab=81.97  E-value=3.2  Score=39.45  Aligned_cols=58  Identities=19%  Similarity=0.173  Sum_probs=39.0

Q ss_pred             CCceeeecccccCCCCCccccCCCCeEeec---CCCCCHHHHHHHhhcC----CCh---hHHHHHHHhc
Q psy938            4 TGDGGLTTPIIESESGEKFGKSARNAIWLD---SKLSSSFELYQYLIRT----KDS---EVYDLLKLFS   62 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~---~~~Tsp~~~yq~~~~~----~D~---~v~~~l~~~t   62 (241)
                      ..+.-...|||.+.+|+||||..|. +.|.   +.--.|..+..|+..+    +|.   ....++.+|.
T Consensus       247 ~~P~f~HlpLi~~~~g~KLSKR~g~-~sl~~~r~~G~~peal~n~l~~lG~s~~~~e~~s~~eli~~F~  314 (490)
T 4g6z_A          247 EVPVYAHLPTVLNEQGEKMSKRHGA-MSVMGYRDAGYLPEAVLNYLARLGWSHGDAEIFTREQFVEWFD  314 (490)
T ss_dssp             CCCEEEEECCEECTTSSBCCTTTTC-CBHHHHHHTTCCHHHHHHHHHTSSBCCTTCCCCCHHHHHHHCC
T ss_pred             CCCeEEEecceeCCCCCcccCCCCC-cCHHHHHHCCCCHHHHHHHHHHhCCCCCCccccCHHHHHhhCC
Confidence            3344467899999999999999875 3332   3334788888888876    232   2355555554

>2v0c_A Aminoacyl-tRNA synthetase; ligase, nucleotide-binding, protein biosynthesis; HET: LMS ANZ; 1.85A {Thermus thermophilus} PDB: 1h3n_A* 1obc_A* 1obh_A* 2bte_A* 2byt_A 2v0g_A*

Probab=81.17  E-value=0.25  Score=50.16  Aligned_cols=32  Identities=19%  Similarity=0.150  Sum_probs=22.5

Q ss_pred             CCC-------CccccCCCCeEeecC--CCCCHHHHHHHhhc
Q psy938           17 ESG-------EKFGKSARNAIWLDS--KLSSSFELYQYLIR   48 (241)
Q Consensus        17 ~dG-------~KmsKS~gn~I~L~~--~~Tsp~~~yq~~~~   48 (241)
                      .+|       +|||||.||.|..++  ++-.++.++=+++.
T Consensus       626 ~~G~~~~~~~~KMSKSkGNvVdP~diI~~yGADalRl~ll~  666 (878)
T 2v0c_A          626 EDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILF  666 (878)
T ss_dssp             TTSSEEEEEEEECSGGGTCCCBHHHHHHHSCHHHHHHHHHH
T ss_pred             CCCCchhhhHHHhhccCCCcccHHHHHHHcCccHHHHHHhc
Confidence            589       899999999997652  12345556656665

>3al0_C Glutamyl-tRNA(Gln) amidotransferase subunit C, GL tRNA synthetase 2; protein-RNA complex, ligase-RNA complex; HET: GSU; 3.37A {Thermotoga maritima}

Probab=80.35  E-value=0.81  Score=44.48  Aligned_cols=40  Identities=18%  Similarity=0.183  Sum_probs=32.0

Q ss_pred             eecccccCCCCCccccCCCCeEeec---CCCCCHHHHHHHhhcC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLD---SKLSSSFELYQYLIRT   49 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~---~~~Tsp~~~yq~~~~~   49 (241)
                      ...|||.+.+|+||||+.|+. .|.   +.--.|..+..|+..+
T Consensus       347 ~hlpli~~~~g~KLSKR~g~~-~l~~~~~~G~~peal~~~l~~l  389 (592)
T 3al0_C          347 MHIPLILGSDRTPLSKRHGAT-SVEHFRREGILSRALMNYLALL  389 (592)
T ss_dssp             CEECCCBCTTSSBCCTTTCSS-BHHHHHHTTCCHHHHHHHHTTT
T ss_pred             EEeeeeeCCCCCcccccCCcc-cHHHHHHCCCCHHHHHHHHHHh
Confidence            588999999999999999983 444   3334788999988775

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	241
d1jila_	323	c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Sta	1e-23
d2ts1a_	319	c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Bac	3e-23
d1h3fa1	343	c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS)	1e-10
d1jh3a_	99	d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-t	2e-08
d1h3fa2	81	d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrR	4e-04

>d1jila_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus aureus [TaxId: 1280]} Length = 323

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Staphylococcus aureus [TaxId: 1280]

 Score = 94.8 bits (235), Expect = 1e-23
 Identities = 43/107 (40%), Positives = 63/107 (58%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G+KFGKS   A+WLD++ +S +E YQ+ I   D +V   LK F+F    
Sbjct: 217 GLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKE 276

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALY 114
            I+  ++     P  R AQK LAE++T  +HGE+ L  A   +QAL+
Sbjct: 277 EIDRLEQSKNEAPHLREAQKTLAEEVTKFIHGEDALNDAIRISQALF 323

>d2ts1a_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Bacillus stearothermophilus, nca 1503 [TaxId: 1422]} Length = 319

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Bacillus stearothermophilus, nca 1503 [TaxId: 1422]

 Score = 93.6 bits (232), Expect = 3e-23
 Identities = 46/103 (44%), Positives = 63/103 (61%)

Query: 8   GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLA 67
           GLT P++    G KFGK+    IWLD + +S +E YQ+ I T D +V   LK F+F S  
Sbjct: 217 GLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKE 276

Query: 68  AIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLAT 110
            IE  +++    PE+R AQK LAE++T LVHGEE L+ A   +
Sbjct: 277 EIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRIS 319

>d1h3fa1 c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophilus [TaxId: 274]} Length = 343

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Thermus thermophilus [TaxId: 274]

 Score = 58.5 bits (140), Expect = 1e-10
 Identities = 21/108 (19%), Positives = 35/108 (32%), Gaps = 11/108 (10%)

Query: 7   GGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSL 66
             L   ++  +  EK  KS  N I L         +++ L+R  D  +    +L +    
Sbjct: 214 CFLMPLLVGLDGREKMSKSLDNYIGLTEP---PEAMFKKLMRVPDPLLPSYFRLLTDLEE 270

Query: 67  AAIEDFKRQNEHKPEERRAQKKLAEDLTLLVHGEEGLKSAKLATQALY 114
             IE   +          A + LA  LT      +         +A Y
Sbjct: 271 EEIEALLKAG-----PVPAHRVLARLLTAAYALPQ---IPPRIDRAFY 310

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 48.6 bits (116), Expect = 2e-08
 Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 5/93 (5%)

Query: 112 ALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISE 171
           AL+S D+ +L    A +  + F             + ++EL ++    P  ++A   I  
Sbjct: 1   ALFSGDIANL---TAAEIEQGFKDVPSFVHEGG-DVPLVELLVSAGISPSKRQAREDIQN 56

Query: 172 GGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRV 204
           G  YVN +++Q+   +L+   H L    T++R 
Sbjct: 57  GAIYVNGERLQDVGAILTAE-HRLEGRFTVIRR 88

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

 Score = 35.9 bits (83), Expect = 4e-04
 Identities = 10/56 (17%), Positives = 20/56 (35%)

Query: 140 ELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHIL 195
             L E  + +  L       P + EA   I   G  ++ + + +P   +  S   +
Sbjct: 11  SELKEGRIWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDLSRPRI 66

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	241
d1jila_	323	Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus au	99.98
d2ts1a_	319	Tyrosyl-tRNA synthetase (TyrRS) {Bacillus stearoth	99.97
d1jh3a_	99	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	99.91
d1h3fa1	343	Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophi	99.88
d1h3fa2	81	Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain	99.77
d1j1ua_	306	Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanoc	99.45
d1n3la_	339	Tyrosyl-tRNA synthetase (TyrRS) {Human (Homo sapie	99.14
d1r6ta2	386	Tryptophanyl-tRNA synthetase (TrpRS) {Human (Homo	99.11
d1p9ka_	79	Hypothetical protein YbcJ {Escherichia coli [TaxId	98.71
d1i6la_	326	Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus ste	98.36
d1kska3	59	Pseudouridine synthase RsuA N-terminal domain {Esc	98.35
d1vioa2	58	Pseudouridine synthase RsuA N-terminal domain {Hae	98.2
d1dm9a_	104	Heat shock protein 15 kD {Escherichia coli [TaxId:	97.81
d1c06a_	159	Ribosomal protein S4 {Bacillus stearothermophilus	96.84
d2uubd1	208	Ribosomal protein S4 {Thermus thermophilus [TaxId:	96.67
d1ffya3	450	Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus	96.48
d2gy9d1	204	Ribosomal protein S4 {Escherichia coli [TaxId: 562	96.4
d1ilea3	452	Isoleucyl-tRNA synthetase (IleRS) {Thermus thermop	96.4
d2d5ba2	348	Methionyl-tRNA synthetase (MetRS) {Thermus thermop	96.39
d1ivsa4	425	Valyl-tRNA synthetase (ValRS) {Thermus thermophilu	96.35
d1rqga2	361	Methionyl-tRNA synthetase (MetRS) {Pyrococcus abys	95.96
d1pfva2	350	Methionyl-tRNA synthetase (MetRS) {Escherichia col	95.72
d1li5a2	315	Cysteinyl-tRNA synthetase (CysRS) {Escherichia col	95.23
d1h3na3	494	Leucyl-tRNA synthetase (LeuRS) {Thermus thermophil	94.57
d1irxa2	317	Class I lysyl-tRNA synthetase {Archaeon Pyrococcus	93.71
d2g1la1	102	Kinesin-like protein kif1c {Human (Homo sapiens) [	81.22

>d1jila_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=99.98  E-value=3.8e-33  Score=252.62  Aligned_cols=113  Identities=39%  Similarity=0.693  Sum_probs=110.2

Q ss_pred             CCCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCC
Q psy938            2 EVTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPE   81 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~   81 (241)
                      ++.+++++|+|||+++||+|||||.||+|||++++||||+|||||||++|++|++|+++||++|.+||+++++.+..+++
T Consensus       211 ~~~~~~~it~pLl~~~~G~Km~KS~~n~i~l~~~~tsP~~~y~k~~n~~D~~i~~yl~~~T~l~~~ei~~l~~~~~~~~~  290 (323)
T d1jila_         211 GQTDAYGLTIPLVTKSDGKKFGKSESGAVWLDAEKTSPYEFYQFWINQSDEDVIKFLKYFTFLGKEEIDRLEQSKNEAPH  290 (323)
T ss_dssp             CCCCCEEEEECCCBCTTSCBTTBCSSSBCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCGG
T ss_pred             ccccceEEecccccchhhhhhhhcCCCCeeeecccCChHHHHHHhhcCCHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCC
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhc
Q psy938           82 ERRAQKKLAEDLTLLVHGEEGLKSAKLATQALY  114 (241)
Q Consensus        82 ~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF  114 (241)
                      +|++|+.||++||+++||+++|++|+++++.+|
T Consensus       291 pr~~Kk~LA~ei~~~~HG~~~a~~A~~~~~~lF  323 (323)
T d1jila_         291 LREAQKTLAEEVTKFIHGEDALNDAIRISQALF  323 (323)
T ss_dssp             GCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHhhC
Confidence            999999999999999999999999999999998

>d2ts1a_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Bacillus stearothermophilus, nca 1503 [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Bacillus stearothermophilus, nca 1503 [TaxId: 1422]

Probab=99.97  E-value=1.8e-32  Score=247.60  Aligned_cols=108  Identities=43%  Similarity=0.689  Sum_probs=103.9

Q ss_pred             CCCceeeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCCCh
Q psy938            3 VTGDGGLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKPEE   82 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~~~   82 (241)
                      ..++||+|+|||+|+||+|||||.||+|||++++||||++||||||++|++|++|+++||++|.+||++++++|.+++++
T Consensus       212 ~~~~~~lT~PLL~~~~G~K~~ks~~n~i~l~~~~tsp~~~yq~~~n~~D~~v~~yl~~~T~~~~eeI~~i~~~~~~~~~~  291 (319)
T d2ts1a_         212 EARAFGLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKEEIEALEQELREAPEK  291 (319)
T ss_dssp             --CCEEEEECCCCCTTSCCTTCCSSCCCBSSTTTSCHHHHHHHHHTCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCTTS
T ss_pred             cccceEeecccccccccceeeecCCCCcccccccCCHHHHHHHhcCCCHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCH
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhccCHHHHHHHHHHH
Q psy938           83 RRAQKKLAEDLTLLVHGEEGLKSAKLAT  110 (241)
Q Consensus        83 ~~~Kk~LA~~i~~~vhG~~~a~~A~~~~  110 (241)
                      |++|+.||++||+++||+++|++|+++|
T Consensus       292 r~~K~~LA~eit~l~HG~~~a~~A~~~s  319 (319)
T d2ts1a_         292 RAAQKTLAEEVTKLVHGEEALRQAIRIS  319 (319)
T ss_dssp             CHHHHHHHHHHHHHHHCHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence            9999999999999999999999999874

>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.91  E-value=1.2e-24  Score=165.26  Aligned_cols=99  Identities=23%  Similarity=0.360  Sum_probs=90.1

Q ss_pred             HhccCCcccCCCCChhhHhhhcCCCceeeeccCCCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          112 ALYSQDLDSLGSLNATDASRIFPGARIVELLMEPGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       112 ~lF~~~~~~~~~l~~~~l~~~~~~~p~~~~~~~~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +||+++   +.+|+++++.+.++++|..++. ..+.++.++|+++|+++|++||||+|+||||+|||++|+|+++.+...
T Consensus         1 ALF~g~---~~~L~~~~~~~~~~~~p~~~~~-~~~~~l~~ll~~~~l~~S~seaRrlI~~ggv~iN~~kv~d~~~~l~~~   76 (99)
T d1jh3a_           1 ALFSGD---IANLTAAEIEQGFKDVPSFVHE-GGDVPLVELLVSAGISPSKRQAREDIQNGAIYVNGERLQDVGAILTAE   76 (99)
T ss_dssp             CCCCSS---STTSCHHHHHHHHTTSCEEEEC-SSCCCHHHHHHHHTSCCSHHHHHHHHHSTTEEETTEECCSTTTCCSST
T ss_pred             CCCCCC---hhhCCHHHHHHHHhcCCcEEec-CCCCCHHHHHHHcCCCcCHHHHHHHHHcCCEEECCEEecCcccccCHh
Confidence            478764   5789999999999999998875 346899999999999999999999999999999999999999999875


Q ss_pred             CcccCCCeEEEEeccccEEEEEEc
Q psy938          192 AHILPNSLTLLRVEVSANIIAKSA  215 (241)
Q Consensus       192 ~~~~~~~~~llr~GKk~~~~i~~~  215 (241)
                       +++++++++||+|||+|++|+|.
T Consensus        77 -~~~~~~~~ll~~GKK~~~~i~~a   99 (99)
T d1jh3a_          77 -HRLEGRFTVIRRGKKKYYLIRYA   99 (99)
T ss_dssp             -TTSSSSEEEEEETTSCEEEEEEC
T ss_pred             -HccCCCEEEEEecCCCEEEEEeC
Confidence             78999999999999999999984

>d1h3fa1 c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Thermus thermophilus [TaxId: 274]

Probab=99.88  E-value=1.1e-23  Score=190.89  Aligned_cols=108  Identities=19%  Similarity=0.131  Sum_probs=97.9

Q ss_pred             CCCCceeeecccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhcCCCHHHHHHHHHHhhcCC
Q psy938            2 EVTGDGGLTTPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFSFDSLAAIEDFKRQNEHKP   80 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t~l~~eei~~i~~~~~~~~   80 (241)
                      ....++++++|+|||+|| +|||||.||+|||++   ||+++||||||++|++|.+|+++||+++.+||+++++.     
T Consensus       208 ~~~~~~~~~~p~L~gldG~~KMSKS~~naI~L~d---sp~~i~~Ki~~~~D~~v~~~~~~~t~~~~~ei~~~~~~-----  279 (343)
T d1h3fa1         208 GQSPQVCFLMPLLVGLDGREKMSKSLDNYIGLTE---PPEAMFKKLMRVPDPLLPSYFRLLTDLEEEEIEALLKA-----  279 (343)
T ss_dssp             TCCCCEEEEECCCBCTTSSSBCCGGGTCCCBTTS---CHHHHHHHHHTSCGGGHHHHHHHHCCCCHHHHHHHHHH-----
T ss_pred             Cccccceeeccccccccccchhhcccccceeeec---hhHHHHHHHhcCCccchhhHHHHccCCCHHHHHHHHHh-----
Confidence            456789999999999999 599999999999999   99999999999999999999999999999999998765     


Q ss_pred             ChHHHHHHHHHHHHhhccCHHHHHHHHHHHHHhccCC
Q psy938           81 EERRAQKKLAEDLTLLVHGEEGLKSAKLATQALYSQD  117 (241)
Q Consensus        81 ~~~~~Kk~LA~~i~~~vhG~~~a~~A~~~~~~lF~~~  117 (241)
                      +++.+|+.||++||+.+||++.+..|.+.+...|...
T Consensus       280 ~~~~~k~~La~~i~~~~~~~~~~~~~~~~~~e~~~~~  316 (343)
T d1h3fa1         280 GPVPAHRVLARLLTAAYALPQIPPRIDRAFYESLGYA  316 (343)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSSCCSCCSHHHHHHTTCC
T ss_pred             CCHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHhhhh
Confidence            4678999999999999999998888887777666543

>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
domain: Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=99.77  E-value=4.5e-19  Score=129.60  Aligned_cols=63  Identities=13%  Similarity=0.132  Sum_probs=57.9

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEc
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSA  215 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~  215 (241)
                      ++|.++|+.+|+++|+|||||+|+||||+|||++++|+++.+..      +++++||+|||+|++|++.
T Consensus        18 i~l~~ll~~~gl~~S~searRlI~~g~V~iN~~ki~d~~~~l~~------~~~~il~~GKK~~~~i~l~   80 (81)
T d1h3fa2          18 IWVARLFTLAGLTPSNAEARRLIQNRGLRLDGEVLTDPMLQVDL------SRPRILQRGKDRFVRVRLS   80 (81)
T ss_dssp             EEHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCEEEC------SSCEEEEETTTEEEEEEEC
T ss_pred             ccHHHHHHHcCCCcCHHHHHHHHHcCCEEECCEEecCccceecC------CCeEEEEecCccEEEEEeC
Confidence            68999999999999999999999999999999999999887654      3578999999999999985

>d1j1ua_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.45  E-value=5.4e-14  Score=124.62  Aligned_cols=92  Identities=17%  Similarity=0.244  Sum_probs=69.9

Q ss_pred             CCceeeecccccCCCC-CccccCCCCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcC------------
Q psy938            4 TGDGGLTTPIIESESG-EKFGKSARNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSF------------   63 (241)
Q Consensus         4 ~~~~~lt~pLL~g~dG-~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~------------   63 (241)
                      .++.+++.|+|+|+|| +|||||.||+|||++   +|+++++|++++       .++.+..+..+|..            
T Consensus       186 ~~~~~~~~~~l~gldG~~KMSKS~~n~I~L~D---~~e~I~~KI~~a~td~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~  262 (306)
T d1j1ua_         186 KKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDD---SPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFG  262 (306)
T ss_dssp             SCCEEEEECCCCCTTCCC-------CSCBTTC---CHHHHHHHHHHSCCCTTCCTTCHHHHHHHHTCCSSEEECCCGGGT
T ss_pred             ccceecccccccCcccccccccccccccccCC---CHHHHHHHHhheeccCCcccCCCchHHHHHhhcccHhhccHHHHh
Confidence            4678899999999999 599999999999999   999999999997       23466777776543            


Q ss_pred             --CCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhcc
Q psy938           64 --DSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVH   98 (241)
Q Consensus        64 --l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vh   98 (241)
                        ++.++++++++.+.++ .+++++|+.||++|++.+.
T Consensus       263 ~~~~~~~~~el~~~~~~g~l~~~~~K~~lae~i~~~l~  300 (306)
T d1j1ua_         263 GDLTVNSYEELESLFKNKELHPMDLKNAVAEELIKILE  300 (306)
T ss_dssp             CCEEESSHHHHHHHHHTTSSCHHHHHHHHHHHHHHHHH
T ss_pred             ccCChhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence              2345678888888766 6999999999999999874

>d1n3la_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tyrosyl-tRNA synthetase (TyrRS)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=2.9e-11  Score=107.92  Aligned_cols=95  Identities=16%  Similarity=0.212  Sum_probs=73.4

Q ss_pred             CCCCceeeecccccCCCCCccccC-CCCeEeecCCCCCHHHHHHHhhcC-------CChhHHHHHHHhcCC---------
Q psy938            2 EVTGDGGLTTPIIESESGEKFGKS-ARNAIWLDSKLSSSFELYQYLIRT-------KDSEVYDLLKLFSFD---------   64 (241)
Q Consensus         2 ~~~~~~~lt~pLL~g~dG~KmsKS-~gn~I~L~~~~Tsp~~~yq~~~~~-------~D~~v~~~l~~~t~l---------   64 (241)
                      ....++++|+|+|++++|.||||| .+|+|||++   +|.++++|++++       .++.+..|++++.|.         
T Consensus       200 ~~~~~~~l~~pll~~l~g~kmsks~~~~~I~l~D---~~~~I~kKI~~a~td~~~~~~~~~~~~~~~~~~~~~~~~~~~~  276 (339)
T d1n3la_         200 GYSKRVHLMNPMVPGLTGSKMSSSEEESKIDLLD---RKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILR  276 (339)
T ss_dssp             TCCCCEEEEECCCCCSSCC-------CCSCBTTC---CHHHHHHHHHTCCCCTTCCSSCHHHHHHHHTTGGGTTCEEECC
T ss_pred             ccCcceeeeeccccccccccccccchhhcccccC---CHHHHHHHHhhccCCCCCcccCccccchhhhccchhhcccccc
Confidence            356789999999999999999987 489999999   999999999997       346677887776542         


Q ss_pred             --------CHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccC
Q psy938           65 --------SLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHG   99 (241)
Q Consensus        65 --------~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG   99 (241)
                              +.++++++++.+.++ .++.++|..||+.|++.+.+
T Consensus       277 ~~~~~~~~~~~~~~el~~~y~~g~l~~~dlK~~la~~i~~~l~p  320 (339)
T d1n3la_         277 DEKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDP  320 (339)
T ss_dssp             CGGGTCCEEESSHHHHHHHHHTTCSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhcCCCCcCCHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence                    123478888888766 79999999999999998755

>d1r6ta2 c.26.1.1 (A:82-467) Tryptophanyl-tRNA synthetase (TrpRS) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tryptophanyl-tRNA synthetase (TrpRS)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.11  E-value=4.5e-11  Score=109.01  Aligned_cols=96  Identities=17%  Similarity=0.232  Sum_probs=78.8

Q ss_pred             CCCceeeecccccCCCC--CccccCCCC-eEeecCCCCCHHHHHHHhhcC-C-----------------C-hhHHHHHHH
Q psy938            3 VTGDGGLTTPIIESESG--EKFGKSARN-AIWLDSKLSSSFELYQYLIRT-K-----------------D-SEVYDLLKL   60 (241)
Q Consensus         3 ~~~~~~lt~pLL~g~dG--~KmsKS~gn-~I~L~~~~Tsp~~~yq~~~~~-~-----------------D-~~v~~~l~~   60 (241)
                      ...+..++.|+||+++|  .|||||..| +|||++   +|.++++|+++. .                 | +.+..|+.+
T Consensus       248 ~~~p~~l~~~~lpgL~G~~~KMSsS~~~s~I~l~D---~~~~i~~KI~~~~~~~~~~~~~e~~~~~g~~~~~v~~~~l~~  324 (386)
T d1r6ta2         248 YPKPALLHSTFFPALQGAQTKMSASDPNSSIFLTD---TAKQIKTKVNKHAFSGGRDTIEEHRQFGGNCDVDVSFMYLTF  324 (386)
T ss_dssp             CCCCEEEEECCCEETTEEEEECCTTSTTCCCBTTC---CHHHHHHHHHHHSCCCSCSSHHHHHHHCCCTTTCHHHHHHHH
T ss_pred             CCCceeeccccccCCCCcccccccCCCCceeeecC---CHHHHHHHhhheeeecCCcccccccccCCCcchhHHHHHHHH
Confidence            45678899999999999  599999865 799999   999999999984 1                 1 235556655


Q ss_pred             hcCCCHHHHHHHHHHhhcC-CChHHHHHHHHHHHHhhccCHHH
Q psy938           61 FSFDSLAAIEDFKRQNEHK-PEERRAQKKLAEDLTLLVHGEEG  102 (241)
Q Consensus        61 ~t~l~~eei~~i~~~~~~~-~~~~~~Kk~LA~~i~~~vhG~~~  102 (241)
                      | ..+.++++++.+.+..| .+++++|+.||+.|++++++-.+
T Consensus       325 f-~~d~~~~eel~~~y~~G~l~~gd~K~~lae~l~~~l~~~re  366 (386)
T d1r6ta2         325 F-LEDDDKLEQIRKDYTSGAMLTGELKKALIEVLQPLIAEHQA  366 (386)
T ss_dssp             H-CCCHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             H-cCCHhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4 35788999999999876 79999999999999999997543

>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: YbcJ-like
domain: Hypothetical protein YbcJ
species: Escherichia coli [TaxId: 562]

Probab=98.71  E-value=3.9e-09  Score=75.69  Aligned_cols=47  Identities=15%  Similarity=0.157  Sum_probs=43.7

Q ss_pred             CCCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          145 PGMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       145 ~~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +.++|.++|..+|+|+|++||+++|.+|.|+|||+.+++|...+...
T Consensus        19 ~~irL~k~L~~~gl~~Sr~eAk~lI~~G~V~VNG~~~~~p~~~V~~~   65 (79)
T d1p9ka_          19 PHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAG   65 (79)
T ss_dssp             SCCCHHHHHHHHTSCSSSSTTSHHHHHHHHEETTBCCCCSSCCCCSS
T ss_pred             CcEEHHHHHHHCCCccCHHHHHHHHHhCCcccCCEEeccccccCCCC
Confidence            45899999999999999999999999999999999999999887765

>d1i6la_ c.26.1.1 (A:) Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Tryptophanyl-tRNA synthetase (TrpRS)
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=98.36  E-value=1.4e-07  Score=83.03  Aligned_cols=82  Identities=21%  Similarity=0.182  Sum_probs=62.5

Q ss_pred             cccCCCC-CccccCCCC---eEeecCCCCCHHHHHHHhhcC-C------------ChhHHHHHHHhcCCCHHHHHHHHHH
Q psy938           13 IIESESG-EKFGKSARN---AIWLDSKLSSSFELYQYLIRT-K------------DSEVYDLLKLFSFDSLAAIEDFKRQ   75 (241)
Q Consensus        13 LL~g~dG-~KmsKS~gn---~I~L~~~~Tsp~~~yq~~~~~-~------------D~~v~~~l~~~t~l~~eei~~i~~~   75 (241)
                      ++++.|| +|||||.+|   +|.|.+   +|.++.++++++ +            ++.+++++.+|..++..+++++..+
T Consensus       183 ~~~~~d~~~kmskS~~~~~~~I~l~D---~~~~i~kKI~~a~td~~~~~~~~~~~~p~~~~l~~i~~~~~~~~~~e~~~~  259 (326)
T d1i6la_         183 IMSLVDPTKKMSKSDPNPKAYITLLD---DAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQ  259 (326)
T ss_dssp             CBCSSCTTSBCCTTCSCGGGCCBTTC---CHHHHHHHHHHCCCCSSCCCCCCTTTCHHHHHHHHHHHHHHCCCHHHHHHH
T ss_pred             eeecCCccccccccCCCccceeeccC---CHHHHHHHHHhhhccccCCccccccCCCCccHHHHHHHHcCCCcHHHHHHH
Confidence            4566777 699999877   699999   999999999996 1            2456666666655544555666655


Q ss_pred             hhcCCChHHHHHHHHHHHHhhcc
Q psy938           76 NEHKPEERRAQKKLAEDLTLLVH   98 (241)
Q Consensus        76 ~~~~~~~~~~Kk~LA~~i~~~vh   98 (241)
                      + .+.++.++|+.||+.|++.+.
T Consensus       260 ~-~~~~~gdlK~~lae~i~~~L~  281 (326)
T d1i6la_         260 Y-EGKGYGVFKADLAQVVIETLR  281 (326)
T ss_dssp             T-TTCCHHHHHHHHHHHHHHHHH
T ss_pred             h-cCCCHHHHHHHHHHHHHHHhH
Confidence            4 456889999999999998864

>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.35  E-value=1.4e-07  Score=63.41  Aligned_cols=43  Identities=16%  Similarity=0.047  Sum_probs=39.2

Q ss_pred             cHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          148 SMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       148 ~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      +|..+|.+.|.+ |+++|+++|.+|.|+|||+.+++|.+.+.+.
T Consensus         2 RLdk~l~~~~~~-SR~~a~~lI~~g~V~Vng~~v~~~~~~V~~~   44 (59)
T d1kska3           2 RLDKFIAQQLGV-SRAIAGREIRGNRVTVDGEIVRNAAFKLLPE   44 (59)
T ss_dssp             EHHHHHHHHHTC-CHHHHHHHHHTTCEEETTEECCCTTCEECTT
T ss_pred             cHHHHHHHcCCC-CHHHHHHHHHcCcEEECCEEeecCCcCcCCC
Confidence            577889988887 9999999999999999999999999988765

>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Pseudouridine synthase RsuA N-terminal domain
domain: Pseudouridine synthase RsuA N-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.20  E-value=6e-07  Score=60.09  Aligned_cols=44  Identities=11%  Similarity=0.120  Sum_probs=39.7

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ++|..+|...+.+ |+++|+++|++|.|+|||..+++|.+.+...
T Consensus         2 mRLD~~Ls~~~~~-SR~~a~~lI~~g~V~Vng~~v~~~~~~v~~~   45 (58)
T d1vioa2           2 LRLDKFIAENVGL-TRSQATKAIRQSAVKINGEIVKSGSVQISQE   45 (58)
T ss_dssp             EEHHHHHHHHHTC-CHHHHHHHHHTTCEEETTEECCCTTCEECTT
T ss_pred             cHHHHHHHHcCCC-CHHHHHHHHHcCeEEECCEEeCCCCCCCCCC
Confidence            4678889888887 9999999999999999999999999888765

>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Heat shock protein 15 kD
domain: Heat shock protein 15 kD
species: Escherichia coli [TaxId: 562]

Probab=97.81  E-value=5.5e-05  Score=56.14  Aligned_cols=64  Identities=14%  Similarity=0.125  Sum_probs=50.5

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEEEEccc
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIAKSANI  217 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i~~~~~  217 (241)
                      .++|...|..+++++|++.|.++|++|.|+|||+++ .|...+..+      ..+.++.|... +.++..++
T Consensus         4 ~mRlD~~L~~~r~~ktR~~A~~~i~~G~V~vNg~~v-Kps~~vk~G------DvI~i~~~~~~-~~i~V~~l   67 (104)
T d1dm9a_           4 EVRLDKWLWAARFYKTRALAREMIEGGKVHYNGQRS-KPSKIVELN------ATLTLRQGNDE-RTVIVKAI   67 (104)
T ss_dssp             CCBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEEC-CTTCBCCTT------CEEEEEETTEE-EEEEECEE
T ss_pred             cEeHHHHHHHhhhHhhHHHHHHHHHcCCeeeCCeec-cccccCCCC------CEEEEEeCCeE-EEEEEEEc
Confidence            478999999999999999999999999999999987 587766654      45678877654 33444333

>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.84  E-value=0.0007  Score=53.62  Aligned_cols=45  Identities=16%  Similarity=0.202  Sum_probs=41.4

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..++..+|+++|..+||.+|.-|-|.|||.+|+-|.+.+.++
T Consensus        51 ~RlD~vv~r~gfa~t~~~arQ~v~Hghi~vNgk~v~iPSy~vk~G   95 (159)
T d1c06a_          51 SRLDNLVYRLGLARTRRQARQLVTHGHILVDGSRVNIPSYRVKPG   95 (159)
T ss_dssp             HCHHHHHHHHTSSSSHHHHHHHHHTSCEEETTEECCCSSCCCCSS
T ss_pred             HHhhhhhccCcccCCHHHHHHHHHhcceEccceEEEecceeecCC
Confidence            457778889999999999999999999999999999999988876

>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=96.67  E-value=0.0018  Score=53.29  Aligned_cols=45  Identities=16%  Similarity=0.186  Sum_probs=41.9

Q ss_pred             CcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          147 MSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       147 ~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      .+|..++..+|+++|..+||.+|.-|-|.|||.+|+-|.+.+...
T Consensus        98 ~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i~vNg~~v~ips~~~~~g  142 (208)
T d2uubd1          98 SRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPG  142 (208)
T ss_dssp             TBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTT
T ss_pred             HHHHHHHHhccccccHHHHHHHHHhcCeecCCeEEEeccEEecCC
Confidence            568888999999999999999999999999999999999988876

>d1ffya3 c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.48  E-value=0.0022  Score=57.57  Aligned_cols=41  Identities=22%  Similarity=0.256  Sum_probs=29.0

Q ss_pred             eeecccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHH
Q psy938            8 GLTTPIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLK   59 (241)
Q Consensus         8 ~lt~pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~   59 (241)
                      .++..++.+.+|+|||||.||+||.+       ++-++.    .+|+.+|+-
T Consensus       388 v~~hG~vld~~G~KMSKS~GN~I~p~-------dii~~y----GaDalR~~l  428 (450)
T d1ffya3         388 LLSHGFVMDGEGKKMSKSLGNVIVPD-------QVVKQK----GADIARLWV  428 (450)
T ss_dssp             EEEECCEECTTSCCCCSSSSCCCCHH-------HHHHHT----CHHHHHHHH
T ss_pred             EEEcceEECCCCCCCCCCCCCCcCHH-------HHHHHh----CcHHHHHHH
Confidence            44557778999999999999999655       343332    456666653

>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

Probab=96.40  E-value=0.0017  Score=53.32  Aligned_cols=46  Identities=17%  Similarity=0.080  Sum_probs=42.6

Q ss_pred             CCcHHHHHHhcCCCCCHHHHHHHHHhCCeEEccEEecCCCCccCCC
Q psy938          146 GMSMLELSLATKCFPRDKEANLTISEGGFYVNYKKVQNPQEVLSPS  191 (241)
Q Consensus       146 ~~~l~~lLv~~gl~~SksEARRlI~qGgV~VNg~~v~d~~~~l~~~  191 (241)
                      ..+|..++..+|+++|..+||.+|.-|-|.|||.+|+-|.+.+...
T Consensus        93 E~RLDnvv~R~gfa~t~~~ARQ~v~Hghi~VNgk~VnIPSy~vk~G  138 (204)
T d2gy9d1          93 EGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPN  138 (204)
T ss_dssp             TTBHHHHHHHHTSSSSHHHHHHHHHTTCEEESSSBCCCTTCBCCTT
T ss_pred             HHHHHHHHhhccccccHHHHHHHHHhcceecCCEEEEeccEeecCC
Confidence            3578889999999999999999999999999999999999988876

>d1ilea3 c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthetase (IleRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Isoleucyl-tRNA synthetase (IleRS)
species: Thermus thermophilus [TaxId: 274]

Probab=96.40  E-value=0.00059  Score=60.45  Aligned_cols=25  Identities=28%  Similarity=0.243  Sum_probs=20.7

Q ss_pred             ecccccCCCCCccccCCCCeEeecC
Q psy938           10 TTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        10 t~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      +...+.+.+|+|||||.||+||+++
T Consensus       391 ~hg~iL~~~G~KMSKS~gn~I~~~d  415 (452)
T d1ilea3         391 CHGLILDEKGQKMSKSKGNVVDPWD  415 (452)
T ss_dssp             EECCEECTTSSCCCTTTTCCCCHHH
T ss_pred             EeeEEECCCCcccCCCCCCCcCHHH
Confidence            3345678899999999999998874

>d2d5ba2 c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Thermus thermophilus [TaxId: 274]

Probab=96.39  E-value=0.00035  Score=59.38  Aligned_cols=26  Identities=15%  Similarity=0.086  Sum_probs=21.7

Q ss_pred             eecccccCCCCCccccCCCCeEeecC
Q psy938            9 LTTPIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus         9 lt~pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      +..-.+.+.+|+|||||.||+||+++
T Consensus       285 ~~~~~~l~~~G~KMSKS~Gn~i~~~e  310 (348)
T d2d5ba2         285 NVGGFLLGPDGRKMSKTLGNVVDPFA  310 (348)
T ss_dssp             EEECCEECTTSSCCCTTTTCCCCHHH
T ss_pred             EeCceEEcccCCCCcCCCCcccCHHH
Confidence            34566778999999999999998874

>d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Valyl-tRNA synthetase (ValRS)
species: Thermus thermophilus [TaxId: 274]

Probab=96.35  E-value=0.00033  Score=61.74  Aligned_cols=23  Identities=30%  Similarity=0.289  Sum_probs=19.7

Q ss_pred             ccccCCCCCccccCCCCeEeecC
Q psy938           12 PIIESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~~   34 (241)
                      -.+.+.+|+|||||.||+||+++
T Consensus       366 g~~L~~~G~KMSKS~Gn~I~~~e  388 (425)
T d1ivsa4         366 GLVLDEKGQKMSKSKGNVIDPLE  388 (425)
T ss_dssp             CCEECTTSSBCBTTTTBCCCHHH
T ss_pred             ceEECCCCCCcCCCCCCCcCHHH
Confidence            34567899999999999999885

>d1rqga2 c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthetase (MetRS) {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Pyrococcus abyssi [TaxId: 29292]

Probab=95.96  E-value=0.0012  Score=56.20  Aligned_cols=18  Identities=39%  Similarity=0.689  Sum_probs=16.0

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      .+|+|||||.||+||+++
T Consensus       305 ~~G~KMSKSlGN~I~~~d  322 (361)
T d1rqga2         305 LEGKKFSTSRNWAIWVHE  322 (361)
T ss_dssp             ETTEECBTTTTBSCBHHH
T ss_pred             eCCEecCCCCCCCCCHHH
Confidence            579999999999998874

>d1pfva2 c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthetase (MetRS) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Methionyl-tRNA synthetase (MetRS)
species: Escherichia coli [TaxId: 562]

Probab=95.72  E-value=0.00083  Score=57.52  Aligned_cols=18  Identities=28%  Similarity=0.263  Sum_probs=16.2

Q ss_pred             CCCCccccCCCCeEeecC
Q psy938           17 ESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        17 ~dG~KmsKS~gn~I~L~~   34 (241)
                      .+|+|||||.||+||+++
T Consensus       290 ~~G~KMSKS~GN~i~~~d  307 (350)
T d1pfva2         290 VNGAKMSKSRGTFIKAST  307 (350)
T ss_dssp             ETTBSCCTTTTCCCBHHH
T ss_pred             ECCeEccCcCCCCCCHHH
Confidence            689999999999998874

>d1li5a2 c.26.1.1 (A:1-315) Cysteinyl-tRNA synthetase (CysRS) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Cysteinyl-tRNA synthetase (CysRS)
species: Escherichia coli [TaxId: 562]

Probab=95.23  E-value=0.002  Score=54.72  Aligned_cols=19  Identities=26%  Similarity=0.164  Sum_probs=16.5

Q ss_pred             CCCCCccccCCCCeEeecC
Q psy938           16 SESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        16 g~dG~KmsKS~gn~I~L~~   34 (241)
                      +.+|+|||||.||.|++.+
T Consensus       261 ~~~G~KMSKs~Gn~V~~~d  279 (315)
T d1li5a2         261 MVDREKMSKSLGNFFTVRD  279 (315)
T ss_dssp             EETTBCCCGGGTCCCBHHH
T ss_pred             ecCCcEecCcCCCcccHHH
Confidence            3589999999999998874

>d1h3na3 c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetase (LeuRS) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Leucyl-tRNA synthetase (LeuRS)
species: Thermus thermophilus [TaxId: 274]

Probab=94.57  E-value=0.0029  Score=56.38  Aligned_cols=40  Identities=13%  Similarity=0.118  Sum_probs=28.6

Q ss_pred             ccccCCCCCccccCCCCeEeecCCCCCHHHHHHHhhcCCChhHHHHHHHhc
Q psy938           12 PIIESESGEKFGKSARNAIWLDSKLSSSFELYQYLIRTKDSEVYDLLKLFS   62 (241)
Q Consensus        12 pLL~g~dG~KmsKS~gn~I~L~~~~Tsp~~~yq~~~~~~D~~v~~~l~~~t   62 (241)
                      -++.+..|+|||||.||.|       +|.++-.+    =..|+.+|+-++.
T Consensus       436 g~v~d~~g~KMSKSlGNVI-------dP~~iI~~----YGADalRl~ll~~  475 (494)
T d1h3na3         436 GTLHLWKPAVMSKSKGNGV-------MVGPFVKE----QGADIARITILFA  475 (494)
T ss_dssp             SSEEEEEEEECCTTTTCCC-------BHHHHHHH----SCHHHHHHHHHHH
T ss_pred             ccEEeCCceeCCCCCCCcC-------CHHHHHHH----hCHHHHHHHHHhc
Confidence            4555667889999999998       78877654    2467777655543

>d1irxa2 c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Adenine nucleotide alpha hydrolase-like
superfamily: Nucleotidylyl transferase
family: Class I aminoacyl-tRNA synthetases (RS), catalytic domain
domain: Class I lysyl-tRNA synthetase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=93.71  E-value=0.0043  Score=50.40  Aligned_cols=20  Identities=25%  Similarity=0.202  Sum_probs=7.3

Q ss_pred             cCCCCCccccCCCCeEeecC
Q psy938           15 ESESGEKFGKSARNAIWLDS   34 (241)
Q Consensus        15 ~g~dG~KmsKS~gn~I~L~~   34 (241)
                      .+-.|.|||||.||+||+++
T Consensus       271 l~ge~~KMSkrkGn~I~~~d  290 (317)
T d1irxa2         271 IKGQKGKMSGSKGNVILLSD  290 (317)
T ss_dssp             ESCC---------CCCCHHH
T ss_pred             ECCccccccCCCCccccHHH
Confidence            33345699999999998774

>d2g1la1 b.26.1.2 (A:498-599) Kinesin-like protein kif1c {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: SMAD/FHA domain
superfamily: SMAD/FHA domain
family: FHA domain
domain: Kinesin-like protein kif1c
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.22  E-value=0.85  Score=31.84  Aligned_cols=33  Identities=24%  Similarity=0.194  Sum_probs=23.6

Q ss_pred             hCCeEEccEEecCCCCccCCCCcccCCCeEEEEeccccEEEE
Q psy938          171 EGGFYVNYKKVQNPQEVLSPSAHILPNSLTLLRVEVSANIIA  212 (241)
Q Consensus       171 qGgV~VNg~~v~d~~~~l~~~~~~~~~~~~llr~GKk~~~~i  212 (241)
                      ..+++|||++|+++ ..+..      +.  .|+.|+..+|++
T Consensus        68 ~~gt~VNg~~i~~~-~~L~~------gD--~I~~G~~~~frf  100 (102)
T d2g1la1          68 GAETYVNGKLVTEP-LVLKS------GN--RIVMGKNHVFRF  100 (102)
T ss_dssp             TCCEEETTEECCSC-EECCT------TC--EEEETTTEEEEE
T ss_pred             CCCeEECCeEccce-eEcCC------CC--EEEECCCEEEEE
Confidence            57899999999754 23332      22  688999887775